I decided to update my games list and trackir software via the menu in the Track IR 4 software with my Track IR 4 pro (I installed the update file with 4.1.037.Final.B I downloaded on the website). After that, every time I launched Lockon Flaming Cliffs 1.12b the blue, red, and green/orange lights would appear just fine, using the TrackIR software to test and align my TIR worked great, but when I launched a mission in Lockon, the lights all appeared fine and TIR software said it detected lockon, but for somereason it didn't work at all. (TIR4 update still worked great with IL2 1946 though). I tried uninstalling and installing TIR5, testing worked with TIR software, but didn't get any lights or indication that Lockon recognized TIR5 at all. I uninstalled all of the above, and reinstalled TIR4 from the CD and everything worked fine.
Just thought I'd let you'll know
