Hello aerlfredith,
What software (Maya, Max, etc.) are you using? I am asking because depending on your workflow, you may be running into trouble with the up axis. Also, let us know which version of the FBX plug-in your are using as well.
Lastly, when you say "my own animation system", what exactly do you mean? Does "system" mean a custom rig? Or, are you using your own software package (i.e. game engine)?
A few more details would be great, then we can start working on your problem.
Cheers,
Carlos