same exe, same input, different output on different servers

I have an application I wrote to take a xen core dump and build a windows crash dump from it, and with the same input file, on one server it runs to completion and on the other it reports errors to the read and write functions... I have md5sum'd the exe and the input file, and both are identical on each server. Does anyone have a hint on where I might start looking for the problem? It's not a disk space issue, both systems are 64 bit, libc is the same version. Is it possible to run strace in such a way that pointers are removed so I can compare the output between runs on the different machines? Thanks James