I've had nothing but good experiences with APPE in Prinergy, I am on version 5 but I don't remember any huge issues with 4. I'd try to contact your Kodak rep and send him some sample files. I was on a PC with version 4 and now I am Mac based using version 5.
The ability that APPE gives you to process transparency is too good to give up on. I'd see if you can somehow work this out with a bit of technical support.
The problem I find is that sometimes it takes a bit of digging to talk to the right person at Kodak. If you aren't on a service contract that can get rather expensive wading through the first couple of layers of phone support til you get the man (or woman) you need.