[AT&T HTC One (M7)] 7175:
Added a couple edits, explained at the end of some paragraphs in case someone comes across this, don't like leaving things incorrect if I know it. I strongly recommend enabling xtrace in the shell to check what's actually being executed, you see your functions and aliases expanded too. With all (busybox ash)|mksh|bash|zsh you can do 'set -x' at any time, append it when calling the shell: 'sh -x' or 'sh -o xtrace' with 'sh' being a symlink to any of the mentioned shells; sh runs the shell in posix mode.

This sounds like SELinux shenanigans. I don't have the HTC One, but I've experienced similar oddities with a SELinux enforced system. (latest TWRP includes SELinux which might be why a twrp doesn't make a difference) With the addition of the SELinux filesystem, a new "file context" permission is attributable to each file/process. The context defines a user, basic function, that it's in the right place, and a sensitivity parameter. There's some good basic info on the SELinux wiki page with commands.

If your system is using enforced SELinux, a program like busybox installed without setting context is going to be denied to exist/run by default, but this depends on how SELinux is configured. I'm guessing it's context is not being set, so it's getting purged on reboot. Another possible SELinux related issue : a custom kernel that doesn't support SELinux is installed on a rom with SELinux --> bad mix, so if that's the case don't be surprised if more issues like this crop up or a data wipe in your sleep randomly occurs out of nowhere --This happened to me twice actually after disregarding this warning-- You can check your SELinux status with

getenforce

-in adb or terminal emu. This should also be displayed in phone info menu in settings. Make sure it's "permissive" or "enforced". Permissive logs warnings of what SELinux would do if enforced. You can change SELinux to permissive with:

setenforce 0

This only works if both your kernel and rom are Selinux compatible. Btw you'll probably find all your SELinux command tools in /system/bin symlinked from toolbox. There's also runcon (run with a context), chcon(change context), restorecon (restore original context), and updates have started integrating a flag (usually -Z) to **filter in** SELinux permissions, e.g. toolbox ls -Z. Busybox does not seem to have updated its tools that could support this, at least on Android. *Even Vanirs busybox 1.22.1.awesome doesn't have the ls -Z function. I was shocked to find out "Toolbox!" was actually useful for something, had a mental breakdown over it a couple months ago. [edit: After reading up on some busybox technical stuff, I found that busybox in its rarely seen full version can in fact be compiled with SELinux extended functions. The reason that almost every rom dev out there uses a busybox that doesn't include every function is portability, case rom to rom ;; older to newer vice versa ;& so that problems will be minimized ;; esac.

**(filters not a good way to put it at 2nd glance, sounds confusing. I mean 'test' or read ACLs<extended perms)

So I would check busybox' context after installing it:

ls -Z "$(which busybox)"

If it's undefined or unconfined, we will change it to this:

u:object_r:busybox_exec:s0

.. We can fix it ourselves over adb or in a su'd mksh/bash shell, (use supersu since cwm superuser does not pass arguments correctly or at all in most situations):

su --shell mksh exec -c mksh -x --

First try to restore original context from file_contexts and see if it works:

restorecon "$(which busybox)"

Then set busybox' context:

sync && mount -w -o remount -t ext4 /system /system
chcon u:object_r:busybox_exec:s0 "$(which busybox)"
sync && mount -r -o remount -t ext4 /system /system

*** added "-t ext4" to mount command- it should then work with toolbox or busybox no errors

The other thing I might guess besides all this SELinux file context stuff is that the installation of the busybox binary didn't write to disk. If you run fsync off in your kernel, a fast reboot soon after busybox installation could very possibly lead to data loss of recent files. Similarly, but without a huge risk of collateral damage, recent changes to files could be lost if you have writeback journaling enabled for /system and you rebooted within (dirty expire + dirty writeback) / 100 seconds. A normal reboot that spends 5-10 seconds dumping and getting everything written to disk should be fine though. IF the new busybox' "mount" applet/function is incompatible or broken or outdated, a mount failure could occur leading to data loss. Backup toolbox mount in /system/bin should be enough to save this though, so I'm sticking with my diagnosis of a "SELinux gotcha".

Hope this helps, nothing worse than losing busybox or su functionality. As a side note, in case this problem takes a few days to figure out, check out Terminal IDE if you haven't before. It is definitely a nice busybox replacement to say the least if you need backup/better primary tools, at least temporarily. It's probably the most valuable app/terminal/busybox/Java/c/c++/ide/apkbuilder I've ever seen. ZERO ads, no net connection. You can get the latest apk off Google code, and there's a thread on xda by the creator Spartacus Rex. The tools and configurations are much more heavy duty than anything I've seen for Android. It has great well written tutorials to walk anybody through java, c, some shell stuff and utilizing ssh,telnet,iirc,git to make using android more like a linux machine. I've really gotten into this so I thought I would mention it.