I presume these external drives are connected by USB?

The overhead for CPU when using USB hard drives can be considerable -
see http://www.extremetech.com/article2/0,2845,1152200,00.asp for an
example.  My guess would be that the various file systems you're trying
will have differing IO requests that _MAY_ be creating different CPU
loads during the scan process - if there is less CPU available for
Squeezebox server / MySQL then this may account for the drop in scan
performance you're seeing.

Any chance you can try it on an eSATA drive?


-- 
Browny

http://www.last.fm/user/BrownySV/
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