I've had similar problems with eps before while watching tenjou tenge from aone. a codec upgrade fixed the problem for me. seeing as you say you have all up to date codecs then what i suggest to you is to try using Gspot and it should tell you exactly which codecs the file uses and which ones you have installed. Sometimes the codec versions are different especially when they release a second version of the same ep.
Get Gspot code info appliance >>HERE<<