Okay...

Windows Media Player 11 (on XP SP2 - up-to-date) - great improvement over the last M$ multimedia flop.
Haali Media Splitter (1.8.122.18) - flawless performance in splitting streams, and seamless, instantaneous decoder execution.
FFDShow (build 2033) - Jesus couldn't have turned out better Win32 decoders with a whole ocean full of water.

But...

1. MP4 playback (either through Explorer or my WMP11 library) takes two tries - first try turns up the typical "Windows Media Player cannot play this file..." crap. Mind you, this is only when I initiate playback, not if MatroskaSplitter is already running.
2. I accidentally set MatroskaSplitter to generate thumbnails at 2500ms instead of 25000ms, and my entire MP4 collection is stuck with sub-black thumbnails, 2500ms into each video regardless that I changed the parameter.
3. WMP11 still hasn't the slightest clue how long the clips are that it's playing, and subsequentially likes to toss the video out half way through in favor of the next playlist item.

However...

I don't believe the problem has anything to do with FFDShow - Haali Media Splitter launches it instantaniously and without gripe.
Instead, I wonder why Explorer isn't recognizing MP4 thumbnails at all, (WMP11 at least loads the wrong thumbnails,) and why WMP11 doesn't list Haali Media Splitter as a plugin.

Pleeeease tell me someone's got the insight to help remedy my multimedia illness! Thanks!

- Brian

(P.S. One [hopefully irrelevent] tidbit of information is that I'm running minlogon [a.k.a. single-user mode] from the XP Embedded package.)

[Edit]
Two new findings...
1. Device Manager reports the location of all Sound, video, and game controllers (Realtek HD Audio aside) to be on "Apple iPod (xxxxxxxxxxx)."
2. If I load MP4 files via. Explorer instead of directly through WMP11 track duration IS reported correctly.
[/Edit]

[Edit]
Scratch problem #1!
I found my solution while picking apart a Vista registry hack to enable MP4 streaming to Xbox 360 (quite a long shot, eh?)
Installing Haali Media Splitter is just one small step short of getting WMP11 to understand that it understands MP4.
One only need to add the following into the Windows XP registry:

Further, I believe I may understand how to enable Explorer thumbnails as well. I hope I'm not the only one who will benefit from these solutions!
[/Edit]

The duration issue when playing things from the library is a bug in WMP. Seeking can also be broken when playing from library.
WMP11 does not show Haali as a plugin, because DirectShow filters are not WMP plugins.

Problem #2 should be fixable by emptying the thumbnail cache. Then Explorer will re-create them.

If you use a proper codec pack, then that will automatically apply the registry tweaks you mentioned, plus several others.