First, thank you for the answer, it is a swing application. The problems occure when loading blobs form an oracle database. I enabled JIT with caching, the second run is faster than the first one, but just half as fast as the binary-code run.
I downloaded the Excelsior JET 3.6 Evaluation Package for windows yesterdays and compiled our application, but the native code seems to be slower than the bytecode. We use a lot of dynamic loaded classes, so i foreced to compile all the libs and the exe-file is now 60 MBs large. Could this be a reason for the performance problems?