After a few hours it seems that CODA for Hand was having a problem. I reverted the DAQ to its old self, got more problems (which were expected as Steve changed the libraries that scaler code was pointing to). After re-pointing all the files to the current system, the DAQ worked fine.
Bottom line, DAQ works fine, but I can't explain why it failed. During the troubleshooting process I killed Coda many times.