I eventually did get them to work late last night. I booted into safe mode, FTP'd to the controller, deleted all files I could, reconfigured the network module, and reinstalled the 6.1.1 software. I then edited the LV-RT.ini file and added serial.dll to the list of OnStartupDLLs. I'm not sure if the last step helped or not because soon afterwards it was removed again, but I did get my serial ports to work. Not sure why they didn't work before.
Thanks though,
Nate