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I dont even use FFDshow anymore as it caused too many issues on my machines to justify keeping it on a finalized HTPC. I only have two codecs installed for my needs right now - Xvid and 3ivx

when you have multiple codecs installed, especially codecs that can decode the same stream type, they tend to 'fight' for priority, or one codec will have a higher priority for that type of stream, when its not the best codec for decoding that type of video. this is where most problems on systems stem from.

Like Infinityloop and ronilse have already stated, only install the codecs you require.