Ok Paul, here's the deal. When I originally checked out the fpc sources I made an fpc folder then individually checked out the utils, compiler, rtl etc folders within the fpc folder. When I did an update I updated the fpc folder, thinking that the subfolders would be updated too. They aren't.
I've updated them all now and recompiled and the autotest I submitted is able to link it in and register properly. My project links it in but isn't able to register, not sure why yet.