Yes, I've seen this kind of behavior a couple of times as well when I
include java or vbscript into a CEWP. It was more prevalent for me in
2003 than MOSS. For example, many people asked for a weather feed on
their home page, and sometimes I found that the script used to display
the external weather was just incompatible enough to cause other things
to break on the page (buttons stopped functioning) or sometimes caused
the web part to close. I never discovered the specifics of what in the
script was causing the problem, but since the problem was consistent and
replicable, this was easy to check in my case by removing the web part
and observing the effect. In your case, since the problem happens
randomly and not that often it would be harder to verify.