When you've got some time flash Tommy's Classic EVO... This is for troubleshooting, I don't expect you to stick with this if you don't want to. Just trying another ROM can narrow some things down for me.
Index of /android/classic/stable
Wipe EVERYTHING manually in recovery (except SD card). Data, cache, dalvik cache, system, boot, SD-android secure, SD-ext
Flash Superwipe
Flash the ROM
When the rom boots and gets set up, download titanium backup from the market.
Dont restore anything! Check out the current numbers for internal and SD-ext.
Download a few large games from the market such as angry birds. Install them.
Check out titanium backup and see what has changed. Internal should move a little bit because of the symbolic link. You may not notice a change in SD-ext because its measured in GB and not MB.
Reboot. check the values again.
Move the dalvik to the SD card.
If everything appears to be working at this point, you know that the partition and dt-a2sd is working just fine. That narrows it down to something that was restored in MikG
I believe restoring that app2SD app and the data with it messed up the partition before dta2SD had a chance to get them moved correctly. Even though the app was not opened the data was restored and it may have corrupted something.