I've been on Windoze for a while now, but in my previous life (6 months ago) I worked on RH Linux, and had some experience with suexec - maybe I can help.

Apache maintains an suexec log doesn't it? Look in the apache logs directory and see if there's an suexec log in there. That log may give some hints as to what's going on - I think it logs every suexec event there.

The apache error log tells you when apache starts and stops, so see if the timing coincides with your flat file ownership change problem.

HTH.