This should be fixed in commit 27f00a9. fstat() as implemented in jnr-posix was calling the unix fd extraction method. On windows we needed to get the HANDLE out of FileDescriptor then open via _osf_openHandle(HANDLE) + _close when done. Seemed to work first try.
Please try this out and reopen if you find this is not working. My only big concern (and this concern overlaps into stat and lstat) is that we seem to be using the 32 bit stat struct. Seems like Windows has like 6 types of stat structs now