I didn't make it!
I have a server which after about 48 hours of running starts lagging out, but once its restarted it runs fine again for another few days. This only started happening after moving over from linux to windows. Is there a bug in the windows binaries, if so is there any knowledge on how to fix this?
There is a memory leak in the Linux dedicated server that causes the server to lag if it is not restarted on a regular basis. Many Linux server providers (like www.escapedturkey.com) have automatic scripted shutdown and restarting to prevent this problem. That's probably why you didn't notice it when you were running under Linux.
It's possible that the JA Dedicated Server for Windows has the same problem, although I've never heard of it before. See if your server provider has the option to have scripted daily rebooting of your server at a time when it isn't busy (like 3 AM).