Well I may have a solution to fix all your woes. For some reason on the stock rom I couldn't get titanium to work correctly due to the infamous "whoami" error. Well he is your fix. We need to reinstall busybox and superuser.
First find your copy of busybox and the Superuser.apk and make sure they are on your SDcard.
1. Reboot your phone into recovery.
2. Goto the partitions menu and mount the /system partition
3. Open up an adb shell and do the following.
We have now reinstalled busybox in case you have mucked something up from the beginning. Now we will deal with Superuser permissions and making them stick.
/system/bin/cat /sdcard/busybox > busybox
chmod 777 busybox
./busybox --install -s /system/xbin
4. Go back to your adb shell.
Once you are back to a "#" prompt in adb recovery:
/system/bin/cat /system/bin/sh > /system/bin/su
/system/bin/chmod 4777 /system/bin/su
After doing these steps you have a couple of things to check out before you are ready to go.
cat /sdcard/Superuser.apk > Superuser.apk
cat /sdcard/su > su
ln -s /system/bin/su /system/xbin/su
chmod 06755 su
5. Reboot your phone into Android.
6. Make sure you see the Superuser app. If you don't you may need to open up the Superuser.apk in Astro and install it. This shouldn't be necessary however.
7. Open up Titanium Backup and make sure it asks you for Superuser permission.
8. If you do then click on the "Problems?" button and let it download the latest busybox into the app's directory.
Once all that is done you should have a fully working Titanium backup you can use, and will probably fix any other su issues you may have been having. Hopefully this helps someone else! Pass it along!!