[G2 and Desire Z General] elusivebyte:
I had something strange happen with the Messaging app, so I may as well list every step I took in case one of them was important.

TL;DR: I backed up "SMS Storage" from stock ROM with Ti Backup then restored it into CM6, but my old messages were still missing. Afterward I backed up and restored CM6 with nandroid and the old messages came back. fix_permissions was used in the middle for unrelated reasons.

I had stock G2 with perma-root and I wanted to try CM6. Without thinking about my apps or their data, I simply did a backup with ROM Manager, wiped and installed CM6. (All in one step. Man, I love ROM Manager!)

When I finally logged into CM6, Android started downloading all the apps I had before. It was then that I realized, "Fuuuuuuuuuck... all my settings and data are gone." I had older backups in Titanium Backup, but I wanted everything to be up to the minute. I also backed up my ADW settings and desktop configuration. Again, what a dream!

I restored my stock ROM backup and used Titanium Backup to backup everything one more time. Then I went through the download, wipe, install process again. It was already downloaded, and ROM Manager was smart enough not to download it again. Nice.

I waited yet again for Android to reinstall all my apps. A couple didn't download right, so I massaged them. I think they had updates with permission changes.

I restored my ADW settings and icons, and launched Titanium Backup. I used the restore screen and the Batch menu option. I clicked on RUN for "Restore All Apps" or whatever, which I knew would prompt me with a giant checkbox list. I unchecked everything and went down the list checking every user app. They were the ones with white text for the most part. If there was a Google system app that I was comfortable restoring, like the data for, say, Goggles, I checked that, too. I didn't check any of the truly system things.

The restore was a success and all my apps functioned beautifully.

I then opened the Messaging app and realized that all my old text messages were missing. Here's where the weirdness more-or-less starts.

I decide to go hunting in Ti Backup to see if I can find the data for the SMS app. I first restored the one with the Messaging app icon, and that managed to restore just my preferences. That made sense afterall, because it was called "[SMS/MMS PREFS] Messaging 2.2.1".

After that I tried restoring the one called "[SMS/MMS/APN] Dialer Storage 2.2.1", thinking that this must be it. No help at all.

I sent a few text messages to one person creating new data.

GPS is broken in CM6, and someone suggested running fix_permissions from the terminal. I did so, and no help with GPS. (But did this maybe fix the SMS data?)

I realized that Swype was missing and someone posted instructions on how to restore it, but you need to be back at stock and pull the files from the stock ROM. (I also could have unzipped the stock rom image, I read later, but anyway...) I restored my old stock backup, ran the ADB commands to pull the files, then restored my CM6 backup I had made just minutes earlier. I use a combination of ADB and Root Explorer to get the files in the right spot and I have Swype again.

I open the first app I can think of to test Swype, and that's Messaging. Bam! All my old messages are back! And my few new ones are now gone!

What's up with that?