[Galaxy Note 10.1 Q&A, Help & Troubleshooting] mitchellvii:
Man this is weird.

Here is the series of events as they transpired:

1. Changed lcd density to 140 in my build.prop file and rebooted.

2. Tablet boot looped.

3. Pulled build.prop and changed lcd back to 160 and tried to push it back to /system/ using adb.

4. Would not push. Received "permission denied" error.

5. Could not get past that error no matter what I did so just ODIN'd back to original root injected firmware as described here: http://rootgalaxynote.com/galaxy-note-10-1-root/how-to-root-galaxy-note-10-1/

6. Tablet then rebooted fine.

7. Touch works perfectly.

8. S-Pen does NOTHING. Tried changing tips, Tried yelling at it. Tried making soft nurturing sounds. Nothing.

9. If I insert the S-Pen into it's dock and remove it the Tablet freezes completely.

10. Went back and completely formatted the SD Card (in case there was anything weird in there causing trouble).

11. Factory wiped, system wiped, wiped everything you can wipe.

12. ODIN'd back to the root injected original firmware.

Still no s-pen.

I thought that maybe by originally changing the lcd density to 140 I had screwed something else. But that build.prop seems to have been replaced with the correct one as seen here:

# begin build properties
# autogenerated by buildinfo.sh
ro.build.id=IMM76D
ro.build.display.id=IMM76D.N8013UEALGB
ro.build.version.incremental=N8013UEALGB
ro.build.version.sdk=15
ro.build.version.codename=REL
ro.build.version.release=4.0.4
ro.build.date=Wed Jul 18 16:53:36 KST 2012
ro.build.date.utc=1342598016
ro.build.type=user
ro.build.user=se.infra
ro.build.host=SEP-101
ro.build.tags=release-keys
ro.product.model=GT-N8013
ro.product.brand=samsung
ro.product.name=p4notewifiue
ro.product.device=p4notewifi
ro.product.board=smdk4x12
ro.product.cpu.abi=armeabi-v7a
ro.product_ship=true
ro.product.cpu.abi2=armeabi
ro.product.manufacturer=samsung
ro.product.locale.language=en
ro.product.locale.region=GB
ro.wifi.channels=
ro.board.platform=exynos4
# ro.build.product is obsolete; use ro.product.device
ro.build.product=p4notewifi
# Do not try to parse ro.build.description or .fingerprint
ro.build.description=p4notewifiue-user 4.0.4 IMM76D N8013UEALGB release-keys
ro.build.fingerprint=samsung/p4notewifiue/p4notewifi:4.0.4/IMM76D/N8013UEALGB:user/release-keys
ro.build.characteristics=tablet
# Samsung Specific Properties
ro.build.PDA=N8013UEALGB
ro.build.hidden_ver=N8013UEALGB
ro.build.changelist=897512
# end build properties
#
# system.prop for smdk4x12
#

rild.libpath=/system/lib/libsec-ril.so
rild.libargs=-d /dev/ttyS0
ro.sf.lcd_density=160

#@SS1 2012-02-10 add property to set max_events_per_sec for model with pen
windowsmgr.max_events_per_sec=60

persist.sys.storage_preload=1
#
##System property for qemu
##
ro.kernel.qemu=0

# System property for Default Brightness
ro.lcd_brightness=140

# Multimedia prop for Smart View
media.enable-commonsource=true

#
# ADDITIONAL_BUILD_PROPERTIES
#
ro.opengles.version=131072
hwui.render_dirty_regions=false
ro.sec.fle.encryption=true
ro.secwvk=220
dalvik.vm.heapstartsize=8m
dalvik.vm.heapgrowthlimit=64m
dalvik.vm.heapsize=256m
ro.config.ringtone=S_Over_the_horizon.ogg
ro.config.notification_sound=S_Whistle.ogg
ro.config.alarm_alert=Good_Morning.ogg
ro.config.media_sound=Media_preview_Touch_the_light.ogg
ro.error.receiver.default=com.samsung.receiver.error
ro.url.legal=http://www.google.com/intl/%s/mobile/android/basic/phone-legal.html
ro.url.legal.android_privacy=http://www.google.com/intl/%s/mobile/android/basic/privacy.html
keyguard.no_require_sim=true
ro.com.android.dateformat=MM-dd-yyyy
ro.com.google.clientidbase=android-samsung
drm.service.enable=true
ro.ril.hsxpa=1
ro.ril.gprsclass=10
ro.adb.qemud=1
ro.com.google.gmsversion=4.0_r2
dalvik.vm.dexopt-flags=m=y
net.bt.name=Android
dalvik.vm.stack-trace-file=/data/anr/traces.txt

As you can see, everything appears to be in order.

So, anyway, I'm stuck on this. Have no idea why S-Pen will not function.