Just for the record, I have the same problem with my WCS Mk II and FLCS. I was initially using the same .B50 files for AH and WB, so I know that they are programmed correctly (after modifying the AH keymap). I have managed to get a pseudo-working solution, but still have trouble with AH dropping keystrokes.
The problem may not be specific to the HOTAS setup, for example, if I start the engine on a plane, and hold down the = key on my keyboard, I will only get one character to register, it will not repeat.
I know others don't have this problem.
Whats strange is that I just updated my PC (new processor, MB, graphics, re-format HD, Win 98, etc) and had the problem with both machines. I have also used two different keyboards with the same results. And finally, I have tried the joystick port on the soundcard and a CH Gamecard.
Maybe the HTC guys can shed some light on what may be different in the input routines between AH and WB.
-- Delta-X