Well I have always been using CoreAVC in MP for all h264 content and ac3filter for spdif (passthrough) sound. So as to answer to your question, I have not changed the video decoder.
And for me this out-of-sync problem persisted with every video which had ac3 or dts sound. So in my case switching to spdifer fixed the problem completely. However I haven't tested this problem extensively: only with coreavc for video, ac3filter for spdif passthrough (and now spdifer for spdif passthrough which fixed the problem.)
(BTW I'm using MP 1.0.2 stable)
And for me this out-of-sync problem persisted with every video which had ac3 or dts sound. So in my case switching to spdifer fixed the problem completely. However I haven't tested this problem extensively: only with coreavc for video, ac3filter for spdif passthrough (and now spdifer for spdif passthrough which fixed the problem.)
(BTW I'm using MP 1.0.2 stable)