Thanks for the suggestion Marco. Unfortunately, I'm stuck with a windows 2003 server. On one hand I would prefer linux, but I am not a server admin and having somebody who can set the environment up for me (and fix things when I break them) is worth it.
I found the mysql config file, my.ini, in Program Files\MySQL\MySQL Server 4.1\
I can't find the line/entry that specifies the timeout in my.ini. I've been googling, searching MySQL's 4.1 documentation... and I can't find anything on how to modify the execution timeout. The only links I find are people (trying) to modify it via PHP... which is NOT what I want to do.
There are several other .ini files in the directory where my.ini is, and they are labled things like my-large.ini, my-small.ini... etc.
None of these files have any mention of the word "timeout", "time out", "time_out" or the value 300 (what the timeout is set to, as mentioned in the error message I get) do not appear anywhere in these files.

WHERE IS THIS #$*#&@! SETTING?!?!?