hmm out of those, i think not wiping properly prior to installation is the one. i didn't install anything on the rom, or change any processor/volt settings.
Yeah that would do it. Not wiping can cause some wacky things to happen, especially when changing between two different ROMs. Minor updates, perhaps going from AOKP 40 to AOKP 41 for example, you may be ok with not wiping (wiping would still be recommended). But going from stock to AOKP would almost certainly require a wipe. And going from AOKP to CM9 would require a wipe as well.
There are many different things you can backup and restore, to make wiping a little less painless. Especially if this is something that you plan on doing often.
Titanium backup - Backup and restores apps, among many other things. Don't restore anything system though. There are alternative apps for TiBu, but to be honest it is the only one I have any experience with.
Alternative homes - Like Nova, Apex, ADW, GO.... many others offer options to save your screen setup and restore.
SMS backup - You can back up your text messages with various apps, some of the alternative SMS clients even allow this if you are user of one of those.
ROM settings backup - There are some ROMs with built in backup options, for their
ROM Control settings. AOKP has an app on the market (
https://play.google.com/store/apps/details?id=com.aokp.backup ). Kernel side there are some options here as well (not backing up the kernel, but the kernel settings).
Probably missed quite a few other things that can help backup/restore. All of this is in excess to the Nandroid backup you make in recovery, it is still recommended you do that....then these are the less necessary ones.