The instructions that come with the Brewmometer also say to keep water off the thermometer housing when using and cleaning the BK. By your description of the glass getting a little cloudy during use it sounds like there's moisture trapped inside there somehow. If it didn't get wet from your use, then are you storing it someplace humid or damp (e.g., your garage) that's not air conditioned?
If there's ever an upgrade to the Blichmann Brewmometer, I'd seriously recommend waterproof housing and better heat shielding be included in the design.