OK, let's see if we can solve this. When I say "test it" below, I mean this: run each of your queries separately (which you know will work) and then test your regular page that queries both tables. After each test, analyze the results. What worked and didn't work. Especially note what worked differently from the previous test. Try to figure out what caused the different behavior. Keep notes of each test. Note what the configuration was, what the test was, what the processing time was, the exact error messages, etc. I know that you think that you will remember all this, but trust me, I've been there, and as the various test configurations and results mount up, you will probably have forgotten some detail that will make a difference in your analysis.
(1) Turn on debugging so that you can see variables, processing time, and SQL statements (and more if you want).
(2) When you "took out" the Timeout value, did you delete the number or did you uncheck the box? Be sure that you have unchecked the box, then test it. Try it with a large timeout value (and the box checked), say 300 seconds (that's 5 minutes). Be prepared to stop and restart the ColdFusion service if it hangs. Note the processing time for the separate tables and also the two-table query. Is one query taking a lot longr than the other? Is that reasonable? BTW, you can override the Timeout value by adding this parameter to your URL: RequestTimeout=n, where n is some integer.
(3) Reboot the ColdFusion host. CF 4.5 has an annoying habit of not returning memory to the OS. The only way to solve that is to reboot. If this solves the problem then you should plan on rebooting periodically, depending on how much traffic there is on your site, or upgrading to CF 5.0.
That's all for now. Write back and report. We'll go from there.