Permalinks work for a short time then break

I have a WordPress site that I’m building on a Windows 2008 server. I am using Helicon Ape rewrite module to enable the pretty permalink structure.

My permalinks will work fine for a couple days then mysteriously stop working. I never get a 404 error, what happens is the URL in the browser will change but the page won’t change. It just stays on the same one.

I thought I had fixed it by going to my Permalinks settings and simply clicking the “Save Changes” button (without making changes to my custom structure). It fixes it every time. The problem is, the issue reappears and I have to keep going back and saving changes. Can anyone tell me what might be going on here?