I have this problem, maybe it started after upgrading to MT 4.2/4.21, I'm not sure.
Its related to the IfCategory tag, that doesn't seem to work; my code is somethik like this, to get a list of URLs of the entries, except those entries with "special" as secondary category:
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Reported on Movable Type 4.2

Sorry, I didn't made the markup... the code is this:
<mt:Entries lastn="10"> <mt:IfCategory type="secondary" label="special"> <mt:Else><$mt:EntryPermalink$> </mt:IfCategory> </mt:Entries>
it should result in a list of all the URLs except those entries with "special" as secondary category; but it outputs all of them instead.
Thanks for your confirmation, Su, at least now I know I'm not the only one with the problem.
I wish it'll be solved as soon as possible…