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Judging by the response in the Megui thread it sounds like Megui is supposed to add Distributor() automatically like VirtualDub and x264 do (and you do not want it called twice).
Oddly not having Distributor() called would cause exactly this behavior, the application that doesn't call it is limited to single threaded performance while other applications that do call it get full multithreaded. I do know VirtualDub (using Avisynth via VFW) calls Distributor() automatically while AVS2pipemod doesn't. Maybe something has changed in your Megui which causes it to not call Distributor() automatically?
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