Thanks for the quick reply!
The US vendor only tested the data logger, using their own converters. I have tried changing out the network cable, thermocouple converters, and thermocouples. None of the changes work so I can't really pin down any problems to any converter. The only thing that is common to the problems I am experiencing is the data logger and the software. I have checked resistances from my thermocouple wires all the way back to the end of my network wire, so I am pretty confident that I don't have an internal broken wire.
With regards to the backward polarity of the thermocouples, I do not believe this is the case since I get exactly the same readings for each channel regardless of the converter or thermocouple installed. This leads me to believe that the data logger isn't really receiving any data and is just spitting out random numbers (currently blank, -25.6, -1.6, -24.1).
Another curiosity, when running autoconfigure to set up any converter, the software will sometimes find the converter, but sometimes it will not. If I change the port that my network cable is plugged into on the data logger I can sometimes get the auto-configure to work.