I've run into a really curious Moksha bug and I'm wondering if anyone else has ever seen it.
Once it hits, Moksha seems to start up more or less normally but in reality seems to have had issues along the way. It'll mostly work and it's still possible to invoke applications, but numerous little things will not work. The Startup Applications don't actually start. Most of the application icons don't load (at first I thought there was an application theme icon issue like was mentioned elsewhere in the forums but when this problem hits no icon themes even show up in the menu in spite of them being installed). Removing the .e folder and reinstalling all the bodhi-desktop and moksha* packages doesn't help. Nothing seems obviously out of place in the regular configuration files in either the home directories or the generic X11 areas, and I've removed / recreated quite a few of them just in case. I've also dumped all the contents of the .cache folder in case of corruption within, but no joy. I'm also not seeing anything in the logs that jumps out as unusual.
Doing a new install does clear it away, and each of the two times I've run into it in the past it coincidentally happened after a new version of Bodhi was already waiting for me anyway, so I took the easy way out. This time I'd like to get a better handle on it if at all possible and ideally see if there's a way to prevent it in the first place.
I suspect (but certainly don't know for a fact) that NoMachine (the NX remote desktop package available from NoMachine) is involved. It doesn't have a well-behaved updater, and I've noticed that in at least two of the three times this Moksha issue has hit me it's happened shortly after one of these NoMachine update attempts. My guess is that it's making some X11 configuration file tweak somewhere that's targeted to Unity but crippling to Moksha, but I've not found it yet. If so, it'd explain why the usual fixes one would try don't seem to work here.