I also encountered the issues with the October 13 patches from Microsoft on Windows 2000.
I removed the sony software, then removed the following patches:
KB840987
KB841533
KB841356
After doing a lot of experimenting, I'm able to use all the MD software with KB841356 installed on Windows 2000 just fine. So, 840987 and 841533 appear to be the culprits.
Interestingly, after removing the patches there now is an ACPI issue with my Windows 2000 box not shutting down when a shut down command is given and instead restarting.
My other PC is Windows XP Professional SP2 and I have no issues with SonicStage 2.2, RealPlayer 10, or Simpleburner 2.