jpilot (if not configured with --with-flock) should use fcntl() instead
of flock(). I don't remember when this option was added.

Can you try to rebuild the Debian unstable version (1.6.2.4-1) and check the 
problem is still present?
Or try to use strace(1) to know why the locking fails.

-- 
jpilot has locking problems over nfs4 and bind mount
https://bugs.launchpad.net/bugs/385388
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