I'm running WCG-BOINC now on almost exclusively IBM machines of various models (T500, X400t, T61p, T61, T60, X61t, T43, T42, M55, M57...) and have noticed no crashing problems.

All are running Windows XP and Lotus Notes 6.5.5

The "heartbeat" graph you see for processor usage is normal. In fact, when you set BOINC to run only at x < 100% of the processor power, it will run at 100% of processor power for x% of the time, causing a characteristic up-and-down graph.

Maybe your cooling is clogged up with dust, causing your machine to actually crash due to overheating? I had that happen on one old desktop machine. The CPU cooler was all clogged up, so that during normal operation it seemed just fine, but while running WCG-BOINC it suddenly started crashing... A good blast of compressed air cleared it out :)

For stabilising Lotus Notes, disable the "Multi-User Cleanup" service. This will prevent "NSD Is Running" errors that might come up.

As for your system tray disappearing, that's a symptom of Explorer crashing. When Explorer crashes, Windows will start it right up again, so all you'll notice is a temporary freeze of your machine, and then the icons in your system tray disappear because the new instance of Explorer doesn't know about them (yet). Some or may will come back after a few seconds, but some system tray icons may stay away "for good".

You should look in your system logs for hints as to what is causing Explorer to crash...