running cm7. using Amon Ra recovery.
Just for the fun of it I made 4 identical nandroid backups. Same apps, same options saved in recovery, nothing added or removed.
3 out of the of the 4 nandroids, when restored, where missing all 6 of the apps stored in my /data/apps folder.
these apps include:

Silent toggle widget
market
a2sdGUI
setcpu
full HDMI app
android keyboard

interesting thing...when I made a nandroid of the ONE that did restore everything...those 6 apps in the folder were not installed on my phone after restoring.

Any idea why this might be happening?
I cleared dalvic, cache...etc

Basically I have one nandroid that has everything I want and restores things properly. But whenever I make a new nandroid, I lose the apps in that folder.

I have even tried clicking every option to save, in recovery...and restored that nandroid, and the apps in that folder are not installed on my phone. Even though they were just prior to making a nandroid.

 

Actually according to froyo apps2sd those exact 6 apps are the only apps I have that cannot be moved to SD, they are on internal memory.

 

Ok, I was able to move all but the market to SD using application settings.