The 3D Glasses do work with an LCD monitor.
The way the '3D Glasses' work is the left and right side of the glasses are darkened for a split second one at a time, during which time the video card driver alters the displayed image to modify the perspective of the 3D scene for the right or left eye. Basically each eye sees the scene from a slightly different perspective.
If you have less then perfect vision they pretty much don't work at all for you.
Also, when using the shutter glasses the refresh rate of the monitor is effectively halved as the eyes see it alternately.
To play a game at 1024x768 with a refresh rate of 85Hz, you would then need top play it at a refrsh rate of 170Hz to get the same experience when using the shutter glasses. So unless you have an incredible monitor it is very strenuous on your eyes to view the image, as in most cases you will be viewing an image that equates to roughly 40Hz.
You should never use the glasses for longer then 20-30 minutes under any conditions as due to the way the brain staggers and adjusts the image your eyes are seeing alternately the stress on your eyes is very significant, and can easily cause nausea and headaches.
If one was to use the glasses for a prolonged period of time they can cause permanent damage to your eyesight.
This is only a brief explanation, but in short experiencing headaches is common when using the shutter glasses, and you should warn your customer about the side effetcs of using said glasses.
The instruction manual for his graphics card should come with a subsection explaining the glasses and how they work, as well as a warning not to use them for long periods of time or if you use prescription glasses.