After 2 days of chatting on IRC, we have come to the conclusion that it was Game2VHBL.prx.
Im baffled that after this much energy & research that it wasn't more evident. :S. Anyways, I just wanted to post here in case someone else has the same problem.
Can someone help me im also having this problem..i downloaded nfl street and it showed ndd olayed perfectly but i deleted it and went to put more iso on my vita ndd i cant see them in adrenaline
The solution was (if I recall correctly) that Sony made an update long ago. This update made it so that we couldn't put files in the GAME folder. They will auto-delete.
The solution? To use GAME2VHBL plugin. This redirects the game folder on the XMB to point to vhbl folder (create vhbl inside psp/) instead of the game folder.