I use smoked glass over my PC monitor and have no problem with the Act Labs PC light gun.
Interesting. Any idea what the transmission of your glass is? Light? Dark? I somewhat expect that the dark plexi discussed in this thread would have a negative impact, but possibly only on range.
Incidently, the Q*bert machine I use as my MAME machine originally had smoked glass over the monitor and clear glass over the smoked glass (It's an upright).
It would be the only choice for a machine where contrast enhancment was desired as well as a graphic bezel. If this were the case on a home machine, you'd need to do it this way too, unless you stuck the graphics to the exterior (bleah

) .
In my case, the machine was barely large enough to accomodate the 27" monitor, so no room for a graphic bezel anyway (it would block parts of the screen.) Therefore, no reason to use both types of glass. But in vertical mode, I have a perfect 19" vertical screen with no screen outline, and in horizontal mode the screen is massive. So it's worth it (to me anyway) to forego the extra decorative touch for something that "feels" right in either mode.
RandyT