Well I discovered my problem. It may not be the same issue for everyone though.
The patch replaced the server launcher batch file, thus erasing any custom settings in there. My server has multiple IP addresses, and one of the settings in the batch file was to tell it which IP to bind to. Since that setting was gone, it was binding to a random IP. When attempting to connect via the favorites list in game it was no longer the correct IP, so no connection >.<
Simple fix. Replace all the options in that batch file. I am not really sure why the patch needed to replace that in the first place though, especially when it did not do anything with the ini.