I've tried passing binary SQLite DBs over the network between different OSes and architectures - it didn't work.
What format are you all using? I've tried an unholy hack of copying SQLite's shell.c and calling shell_main() with a hacked up argc, argv, stdin with success on Mac. Pity I'm developing for the iPhone and it fails only there.
Does everyone do such awful things?
This is one of the core features of SQLite.
http://sqlite.org/different.html
Check the code that's passing the databases. Do a byte-by-byte comparison to make sure they're equal after transfer. This definitely should be working.
Beyond Compare has good binary file comparison support.