If I read things correctly, the flasher is appearing on the "Open Windows" portion of the Start bar(?). The normal setup is the Start Button at the left, with a "Quick Start" bar next with shortcuts to a few programs, the larger center area where there's a button for each Window that's open, and the SysTray with icons for the Startup processes.
It the "flasher" is in the central "Open Windows" part of the bar, it should mean that whatever is running is opening a Window, and you might catch more of a glimpse of it if you can arrange to observe it when there are no other Windows (programs) on the screen. It is possible to set a program to "Open Minimized," so the button may still be the only thing that would appear.
Most processes that open and then close themselves appear only as flags that pop up from an icon in the SysTray part of the bar. About the only things I've seen that actually open a window that closes itself are generally something to do with external connections, usually to the web. This may narrow it down to a browser or email action, but the action could be triggered by any program that wants to call out. Your email checks are as good a guess as any, probably.
You mentioned earlier that you found 51 running processes. That's not a remarkably high number, but I seldom see more than about 45. I currently see only 41 with 5 program windows open, LAN connection, and a couple of USB devices running in addition to the usual Windows things.
WinXP actually does quite a lot of "logging" of what's running, and theirs an "error logger" built in that you can turn on to record what's happening, for troubleshooting. I don't use them often enough to suggest where to look without some research.
Start | Help | Index and and "Event Viewer" in the topic box may be a place to start, if the "flash" is associated with an "error" that gets logged. The built in error recorder, that you can turn on or off, is called "Dr. Watson" which might be another topic to look at. Neiter of these are likely to record anything that's a "normal" process, but they're places to look if things get desparate.
Stilly -
I find that the WinXP Firewall does a good job of blocking java and popups, and nearly always gives you enough time to "enable for this page" to avoid missing out on anything essential. Unfortunately (IMO) a lot of the diagnostics, drivers, and utility download sites do require !$%##! java to function now. It works just fine behind my other firewall (on another net-connection machine) but multiple firewalls on the same machine might cause some conflicts(?).