[Nexus 7 3G Android Development] Synman:
Yup, Trusted Face is busted.... will need to look into it.... might be a GAPPs issue might not be ... I'm using PA MICRO GAPPS.

I/ActivityManager( 508): START u0 {cmp=com.android.facelock/.SetupIntro (has extras)} from uid 10019 on display 0
W/AudioTrack( 508): AUDIO_OUTPUT_FLAG_FAST denied by client
I/ActivityManager( 508): Start proc com.android.facelock for activity com.android.facelock/.SetupIntro: pid=14700 uid=10027 gids={50027, 9997} abi=armeabi-v7a
D/OpenGLRenderer(13142): endAllStagingAnimators on 0x5b31a438 (ListView) with handle 0x614e0188
D/OpenGLRenderer(14700): Render dirty regions requested: false
D/Atlas (14700): Validating map...
D/libEGL (14700): loaded /system/lib/egl/libEGL_tegra.so
W/SurfaceFlinger( 131): couldn't log to binary event log: overflow.
D/libEGL (14700): loaded /system/lib/egl/libGLESv1_CM_tegra.so
D/libEGL (14700): loaded /system/lib/egl/libGLESv2_tegra.so
I/OpenGLRenderer(14700): Initialized EGL, version 1.4
D/OpenGLRenderer(14700): Enabling debug mode 0
I/ActivityManager( 508): Displayed com.android.facelock/.SetupIntro: +557ms (total +21s457ms)
I/art ( 508): Explicit concurrent mark sweep GC freed 34129(1744KB) AllocSpace objects, 9(144KB) LOS objects, 33% free, 20MB/31MB, paused 1.287ms total 89.677ms
W/AudioTrack( 508): AUDIO_OUTPUT_FLAG_FAST denied by client
W/AudioTrack( 508): AUDIO_OUTPUT_FLAG_FAST denied by client
I/ActivityManager( 508): START u0 {flg=0x2000000 cmp=com.android.facelock/.SetupFaceLock (has extras)} from uid 10027 on display 0
F/libc (14700): Fatal signal 4 (SIGILL), code 1, fault addr 0x69eaa09a in tid 14700 (ndroid.facelock)
I/libc (14700): Suppressing debuggerd output because prctl(PR_GET_DUMPABLE)==0
I/WindowState( 508): WIN DEATH: Window{aaee859 u0 com.android.facelock/com.android.facelock.SetupIntro}
I/Zygote ( 143): Process 14700 exited due to signal (4)
I/ActivityManager( 508): Process com.android.facelock (pid 14700) has died
I/ActivityManager( 508): Start proc com.android.facelock for activity com.android.facelock/.SetupFaceLock: pid=14722 uid=10027 gids={50027, 9997} abi=armeabi-v7a
F/libc (14722): Fatal signal 4 (SIGILL), code 1, fault addr 0x5ed4309a in tid 14722 (ndroid.facelock)
I/libc (14722): Suppressing debuggerd output because prctl(PR_GET_DUMPABLE)==0
I/Zygote ( 143): Process 14722 exited due to signal (4)
I/ActivityManager( 508): Process com.android.facelock (pid 14722) has died
I/ActivityManager( 508): Start proc com.android.facelock for activity com.android.facelock/.SetupFaceLock: pid=14739 uid=10027 gids={50027, 9997} abi=armeabi-v7a
F/libc (14739): Fatal signal 4 (SIGILL), code 1, fault addr 0x5ed4309a in tid 14739 (ndroid.facelock)
I/libc (14739): Suppressing debuggerd output because prctl(PR_GET_DUMPABLE)==0
I/Zygote ( 143): Process 14739 exited due to signal (4)
I/ActivityManager( 508): Process com.android.facelock (pid 14739) has died
W/ActivityManager( 508): Force removing ActivityRecord{1da9fc2a u0 com.android.facelock/.SetupFaceLock t236}: app died, no saved state
W/WindowManager( 508): Failed looking up window
W/WindowManager( 508): java.lang.IllegalArgumentException: Requested window android.view.ViewRootImpl$W@2dbe8ce does not exist
W/WindowManager( 508):	at com.android.server.wm.WindowManagerService.windowForClientLocked(WindowManagerService.java:8417)
W/WindowManager( 508):	at com.android.server.wm.WindowManagerService.windowForClientLocked(WindowManagerService.java:8408)
W/WindowManager( 508):	at com.android.server.wm.WindowManagerService.removeWindow(WindowManagerService.java:2558)
W/WindowManager( 508):	at com.android.server.wm.Session.remove(Session.java:186)
W/WindowManager( 508):	at android.view.ViewRootImpl.dispatchDetachedFromWindow(ViewRootImpl.java:2920)
W/WindowManager( 508):	at android.view.ViewRootImpl.doDie(ViewRootImpl.java:5390)
W/WindowManager( 508):	at android.view.ViewRootImpl$ViewRootHandler.handleMessage(ViewRootImpl.java:3223)
W/WindowManager( 508):	at android.os.Handler.dispatchMessage(Handler.java:102)
W/WindowManager( 508):	at android.os.Looper.loop(Looper.java:135)
W/WindowManager( 508):	at android.os.HandlerThread.run(HandlerThread.java:61)
W/WindowManager( 508):	at com.android.server.ServiceThread.run(ServiceThread.java:46)
W/InputMethodManagerService( 508): Got RemoteException sending setActive(false) notification to pid 14700 uid 10027

I maintain an app of my own that relies on JNI and am not having any issues with it. I'll look into the error you described and see what OmniROM did to address it. FYI Lil' Debi does not work for me either but I don't get anything meaningful via Logcat from it:

I/LilDebi (13240): exec: su -s /data/data/info.guardianproject.lildebi/app_bin/sh
I/LilDebi (13240): writeCommand: cd /data/data/info.guardianproject.lildebi/app_bin
I/LilDebi (13240): writeCommand: ./create-debian-setup.sh /data/data/info.guardianproject.lildebi/app_bin /storage/emulated/legacy /storage/emulated/legacy/debian.img /data/debian \
I/LilDebi (13240): && ./stop-debian.sh /data/data/info.guardianproject.lildebi/app_bin /storage/emulated/legacy /storage/emulated/legacy/debian.img /data/debian \
I/LilDebi (13240): && ./unmounted-install-tweaks.sh /data/data/info.guardianproject.lildebi/app_bin /storage/emulated/legacy /storage/emulated/legacy/debian.img /data/debian \
I/LilDebi (13240): && ./start-debian.sh /data/data/info.guardianproject.lildebi/app_bin /storage/emulated/legacy /storage/emulated/legacy/debian.img /data/debian \
I/LilDebi (13240): && /data/data/info.guardianproject.lildebi/app_bin/chroot /data/debian /data/data/info.guardianproject.lildebi/app_bin/complete-debian-setup.sh /data/data/info.guardianproject.lildebi/app_bin /storage/emulated/legacy /storage/emulated/legacy/debian.img /data/debian
I/LilDebi (13240): writeCommand: ./stop-debian.sh /data/data/info.guardianproject.lildebi/app_bin /storage/emulated/legacy /storage/emulated/legacy/debian.img /data/debian
I/LilDebi (13240): writeCommand: exit
I/LilDebi (13240): Done!
I/ActivityManager( 508): START u0 {act=android.intent.action.VIEW flg=0x10 cmp=info.guardianproject.lildebi/.LilDebi} from uid 10080 on display 0
D/AndroidRuntime(13598):
D/AndroidRuntime(13598): >>>>>> AndroidRuntime START com.android.internal.os.RuntimeInit <<<<<<
D/AndroidRuntime(13598): CheckJNI is OFF
W/app_process32_o(13598): type=1400 audit(0.0:791): avc: denied { write } for name="system@framework@boot.art" dev=mmcblk0p10 ino=229381 scontext=u:r:shell:s0 tcontext=u:object_r:dalvikcache_data_file:s0 tclass=file
I/ToolbarWidgetWrapper(13240): Progress display unsupported
I/LilDebi (13240): savedInstanceState was null
I/LilDebi (13240): Not upgrading '/data/data/info.guardianproject.lildebi/app_bin'
I/LilDebi (13240): Installing busybox symlinks into /data/data/info.guardianproject.lildebi/app_bin
I/LilDebi (13240): /data/data/info.guardianproject.lildebi/app_bin/busybox --install -s /data/data/info.guardianproject.lildebi/app_bin
E/PhoneWindow(13240): Circular progress bar not located in current window decor
E/memtrack(13598): Couldn't load memtrack module (No such file or directory)
E/android.os.Debug(13598): failed to load memtrack module: -2
I/ActivityManager( 508): Displayed info.guardianproject.lildebi/.LilDebi: +169ms
D/AndroidRuntime(13598): Calling main entry com.android.commands.am.Am
D/AndroidRuntime(13598): Shutting down VM
I/art ( 508): Explicit concurrent mark sweep GC freed 35752(1754KB) AllocSpace objects, 2(32KB) LOS objects, 33% free, 19MB/29MB, paused 2.313ms total 108.417ms

I wonder if my native you mean an actual native app vs something called via JNI? Will look into OmniROM shortly.

I have stericson's busybox pro.... and am able to recreate this issue. It looks like a timing issue between it and SU. I used ChainFire's fastboot boot loader to root. Let it finish its initial cataloging of "Smart Install" then close it out completely (swipe it from recent apps), open it back up, and the install will work fine.