Annie,
I haven't personally used the Topcon GMS-2 so the best I can offer is two suggestions:
1. Make sure that another program on the device isn't utilizing the GPS as well. I'm sure the Topcon has some sort of utility to connect to the gps. Within that program reset the gps, then disconnect. Try to connect to ArcPad.
2. Perform a factory reset on the device. If you haven't wiped the device clean in quite a while I'm sure it's due for it. Shouldn't take more than 30 minutes to perform the reset and get ArcPad installed again.
If neither of these work respond back with the protocol, port, and baud rate you're attempting to use.