NesterJ and Snes9x Problem

[yalkara]

Hi, I installed both NesterJ and Snes9x, they both work flawlessly so far except for one thing.

No matter where I put them, the rom's keep over writing each other.
I made a folder for the nes ones and one for the snes ones, I put the nes ones in the nes folder and the snes ones in the snes folder.
However the snes ones over wrote the nes rom's.
I then copied my nes rom's back over to my psp into the nes folder, and they over wrote the snes ones this time.

Is there any way to get both set's of rom's working without them over writing each other?

Also yadda yadda, I own all the games I've got rom's for, blah blah legal stuff.

Edit: Incase it matters, I am running 5.00m33-4 on a Phat PSP with iR Shell 4.8
NesterJ is v1.11 and Snes9xTYL test version 5