I have the Gen 1 Flirc and have the same issues. Turns out the latest Windows Flirc software (v3.25.4) doesn't include the driver.
I had to install an older version (3.25.2) and it had the drivers bundled. See this thread: http://forum.flirc.tv/index.php?/forum/96-flirc-gen1-sticky/
After installing v3.25.2, I could launch the Flirc companion app and upgrade the firmware, set key presses, etc, like usual.