What are your comps' specs? What other processes do you have running? What does the task manager say about processor and memory usage for applications running on your computers before and during the anomoly? How many files do you have in your solution/projects? That's interesting that it happens on both of your computers.
I've noticed that 2003 ussually takes a few minutes to start up for the first time for the day (my theory is that it is loading the quick help MSDN stuff) but other than that, I haven't noticed any major slow downs that weren't related to something else going on on my computer, such as seti@home or a defrag.