As a last consideration, there are some automation alternatives for using Profiler. If you're a dyed-in-the-wool Books Online aficionado, you know you have a bunch of stored procedures you can invoke to run Profiler (sp_trace_setfilter to get them set up and sp_trace_setstatus to stop them). But if you are after the creature comforts, you can schedule your trace selections as jobs by having Profiler create the scripts for them. This is infinitely more convenient, not to mention less frustrating, because the system stored procedures that control traces are very particular in the way they accept parameters. Then again, if you weren't very particular, you wouldn't be use the stored procedures in the first place!
Using the scripting facility to create scheduled jobs is an enormously helpful feature. Once you know what you want, you can have the jobs engine start and stop jobs for you. The only change you have to make to the script file is to change the name of the target directory where the output will be saved. Note that you can pepper your trace with the panoply of Show Plan variants, so that you're sure to get the information you need to determine how things are working (or not working).