2phless, I was having the exact same problem. It was also happening to me because of a different issue in the new version im writing.
UPDATE - For all of those who wished that this would bridge the UTEC to your other external WBO2, your day is comming very soon. I am currently adding support into the program for it, and as soon as I get a log from somebody who has one then I can seal the deal.
Here's what you do: Sync up with your WBO2 via hyperterminal. Capture everything to a text file, just like when you are using the utec and logging. Capture everything that you do wiht the wbo2, starting from the moment you connect up through the point where it is logging on your screen. Once you get that, stop the capture and email me the file. With that I can analyze what's going on communication-wise and code appropriately.
Email to: email@example.com
More things have been added, such as the ability to modify the logger-1 output by replacing the stock ignition value with your coolant temp or air intake temp. This only works when you are in dashboard mode and will move over the ecu ignition value to where your utec timing value is, whenever it would say "ECU". I have recently made it so that the autologger doesnt capture lines while you are in termination delay, but im going to make it an option in the settings. With it on you can use it to gauge how fast you shift or how low your boost drops or whatever else you might want to see it for.
Hopefully I'll have it out tomorrow, with or without the Bridge function. Its all up to you guys!