What would cause IIS to return a 404, only sometimes? If I hit a 404 on a page, I can simply hit refresh and it will come up. It's reproducible. I've used fiddler to see what's going on and I don't see anything off. I've setup IIS tracing but again, I don't see what exactly the issue would be, the file exists and the 404 only occurs sometimes. By sometimes I mean if I navigated to a page and got a 404 I could refresh and it would come up but other times I could navigate to that page and it would not 404. It isn't limited to any one page or condition.
What other things can I try to determine what the issue is?
If you've run Fiddler and you see the request arrive at the server and you see a 404, then this doesn't sound like a web farm problem.
You might want to try SysInternals ProcMon to see what's going on underneath.