The idea with a stack trace is often to take several in a row and just look for patterns. I see the one running thread in your stack that you provided was waiting for class loader hard drive access while creating an object. “java.io.FileInputStream.open”
If all your stack traces seem to be waiting on file I/O, is there anything on your computer that would be slowing down the hard drive a lot? Also, has ColdBox always been this way, or did the behavior just start?
You mentioned that you have 4 Gigs of RAM installed on your machine. How much memory is being used normally? I’ve seen excessive swap usage really slow a machine down, but that wouldn’t necessarily manifest itself in your stack trace as I/O because Java doesn’t actually know when the OS swaps out RAM to disk.
Thanks!
~Brad
I took several stack traces in a row and they all had java.io.FileInputStream.open in them. As far as something that might slow down my hard drive, my company requires hard drive encryption on all laptops so that might be it. On an old laptop I had the encryption software installed on I probably saw it slow down by 25%. It is a pain in the rear.
Now if I remember correctly, CF takes all the CFM/CFC files and compiles them to Java class files, correct? I assume that this might be where I’m running into issues? If this is indeed the problem, I have access to an unencrypted network drive that I can try running CF from. Perhaps that might fix my issue.
As far as memory usage, when I’m running all my dev software (CF, CF Builder, SQL Server, etc.) I use up most of the 4 gig of RAM. I’ve recently been having CF hit a dev MSSQL box instead of my local MSSQL install just so I can save the memory by having it disabled.
I figured out how to fix this problem: simply turn off the ColdFusion setting to save class files to disk. Everything is working great now. My guess would be that running off an unencrypted drive might have worked too but this is much easier.
Thank you very very much for the help!
Dustin, be sure to also flush all these thousands of class files that Brad mentioned. Once you end up thousands of them, you’ll be experiencing slow file system crawls which may be the reason why you had problems, add the file system encryption on top of that and as you now know, it’s no picnic! 
BTW, Thanks for reporting back how you solved the problem. Cheers.