I don't know if this has anything to do with it, but iirc a while ago many people were having problems transferring the apps generated by TI-Boy over USB (I think this problem still exists), but they seemed to work fine over a serial/parallel link cable (ie through the I/O port).
I for one know that I cannot get a large (as in Pokemon-sized) app to transfer correctly to my 84+SE over USB (it errors when it starts validating), and I have one with all the extra RAM. However, if what calc84maniac says is true, this may be the source of the actual problem: the app itself is not getting converted into the proper form by Rabbitsign.
Or it could be just as simple as your antivirus

.