The error message means that the software sent a mode 3 request (get trouble codes) and the scantool responded, but the software didn't understand the data.
There may be some subtle differences between the various ELM chips that the software isn't accounting for. (I tested the program on a '97 Pontiac Bonneville, which uses the VPW protocol)
Try rerunning the software using the /debug command switch, then try reading the troublecodes. It should still come up with the same error, but this time it'll generate a log file (obd.log).
Email me a copy of the log file (send it as a file attachment), then hopefully I'll be able to sort out what it all means.