Difference between formatting & wipe Is there any difference in "wipe" (from the recovery mod) and factory reset from the android OS?

Does factory reset/wipe remove the custom ROM?

I need to know because after doing the "ALL wipe" from ultrajack recovery, I flashed a ROM. But the old boot animation, the system apps all remain!!

How can I fix this? or should I manually remove the system apps by mounting it as Rw. etc etc?
A factory reset won't remove a custom ROM unless the backup image in the custom ROM is for a ROM other than itself.  This would be pretty unlikely.

I think we'd need to know your phone model and the ROM you used to help you figure out why it didn't write over the system apps.  That's definitely not normal.  Normally virtually no trace of the old ROM should be left.