44.1/16 is v. standard and is played directly by jFlac and have no
problems.

Have your problem files been compressed by a non standard encoder ?  

You can test by re-encoding the problem files with standard Flac at a
lower bit rate to see if problem goes away.

Highly compressed file take longer to decode at startup and could
explain your initial "stutter" - again test with a re-encoded problem
file to isolate the issue.


-- 
bpa
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