This bug has also been bothering me for a while now and it only seems to happen on those feeds you just can't let go of :(
So I looked and looked for a solution and only recently found two, between them I am hoping they will clear up this problem. Both are extensions although one is more of a bug fix wrapped in an extension.
1st - Thunderbird RSS Feed Item Unique Identifier Patch available from http://dawis.icb.uni-due.de/?id=245
This creates a unique identifier within thunderbird and then uses to check for new ones, instead of relying on what the server is telling it.
2nd, Remove duplicate Messages available from https://addons.mozilla.org/en-US/firefox/addon/956
if you get any duplicates through this patch will clean it up for you, and has a few config options.
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