If you look at the master cylinder from the left side of the handlebars (normal seating possition) you should be able to see a small hole (rectangular) at the joint face, between the reservior and the cover. The hole is just above the rubber gasket. This hole allows atmospheric pressure between the cover and rubber gasket. If the hole is blocked off by dirt, any debris, your brakes are not going to work properly.
In a clean, dry environment (the garage is fine) remove the cover and the rubber gasket. Wipe them clean and make sure to clear the area where you see the hole in the edge of the cover, with a lint free cloth. Then reassemble the gasket and cover. This was posted here by someone else. It worked for me and if you think about it, it makes a lot of sense.
Good luck,
Chuck
PS. I forgot to mention, this works for the master cylinders made of metal. Not sure if this will help you with the plastic units...