This bug has caused me hours of headache and frustration. More than I could possibly describe in a reasonable post. So for the sake of keeping this post on-topic, I'll just describe this bug in Velocity 0.3:
"mms" script. Or possibly others, mms is just the last app I removed that I later tried to reinstall.
"busybox cp /system/app/Mms.apk /sdcard/.velocity" line (under the "-rm" block)
If the ".velocity" folder doesn't exist on the SD card, it ends up copying the "Mms.apk" file to a file named ".velocity". Then when you go to restore, it checks if "/sdcard/.velocity/Mms.apk" exists, and it doesn't (.velocity is a file).
So basically it totally trashes the apps that you remove, no backup, do not pass Go, do not retain one's sanity.
I was able to restore Mms.apk by renaming .velocity to .velocity/Mms.apk then running the script (just copying the Mms.apk file and running "sync" didn't seem to fix it, hence hours of frustration). But my phone still isn't storing incoming texts. It receives them, pops up a notification with the latest message text, but the message is not stored in the database (com.android.providers.telephony), so neither Handcent nor the native Messaging app can see what was just received. So pissed off with this ROM right now. Mixed blessing, lots of good stuff, but the bad things are SO bad they're overshadowing everything... /ugh
Thanks for the work on this ROM none the less. Certainly not something I could have done myself.