So it runs slower compiled with OwlWare than uploaded with OwlProgram? Master branch?
It is probably because key memory sections have ended up on the heap, ie external RAM.
Looking at the code, it seems that the Patch object is created on the heap (FactoryPatches.cpp:25).
If you don't need the external RAM you can change line 24 to
This sets up 64kB of internal ram as heap.
Come to think of it, are you compiling in debug mode? Try with
make CONFIG=Release and see if it doesn't speed things up!