I had the same problem. I assumed it was a Linux permissions issue with executables created by FPC on NTFS disks. If I compile a linux executable under Windows/NTFS and then copy it to a linux partition, it won't run unless I 'make it executable' under Linux.
In the end I just cloned my dev folders from the NTFS disk to the Linux one.
If there's an answer to fix the issue, I'd like to know..