I was away for 1.5 days, so could not reply.
First screenshot shows the different video and audio formats you can decode using ffdshow. You uncheck the ones you want to decode using other modules. For example, I have found that DTS and AC3 are decoded and downmixed properly only with AC3filter. Also uncheck the "tray icon" box, so that it does not clutter the systray and possibly force BSPlayer out of full screen mode.
Second screenshot is pretty self-explanatory. You may leave all options untouched.
Release is valid for both WinXP and Win98 (as I wrote before). But you may choose Release Unicode if you don't plan using Win98.
video is a bit slow :: What is the CPU usage while you play the video? You can see CPU usage using, for example, WinXP 'Task Manager' (taskmgr.exe). If CPU usage of BSPlayer.exe is at 90% or higher, then you must find out which option eats the CPU. It could be video post processing. Uncheck that in ffdshow properties.
video out of sync :: I have never experienced out of sync with this configuration – Gabest's Matroska splitter + ffdshow + ac3filter/uncompressed/mp3. It didn't show up with native H.264, nor with H.264 in VfW mode (with delay frames). Video will be desynced from time to time if your CPU cannot keep up, but the delay will not be constant.
What is the video format of files in question? (MKV is not a video format.) If you're using ffdshow, you can see it under this path while a file is currently playing.
Options -> Filters -> ffdshow MPEG-4 Video Decoder -> Info & debug
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To all :: I wonder if Haali could have treated the videos in some special way, automatically resyncing audio with video...
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