Here is a quick test to show if the gantry is in fact flexing.
Place a heavy chunk of metal in the center of the table. I used channel iron. Mount a magnetic base dial indicator on the metal and zero it to the bottom of the gantry, in the center. Do this with the Y car to one side. Now move the Y car to the other side and watch the dial indicator. Is the gantry flexing as the weight of the Y car and router/spindle is moved from one end of travel to the other? You can also push down on the gantry a little and watch the dial indicator.
Another good test to run would be to set up as explained above and turn on your vacuum pump. Watch the Trupan spoilboard change thickness over the next half hour to hour. I expect you will get a lot of movement in the first 1/4 hour and the movement will slow after that..
The tests above test for two different things. Either one or both together will cause your cut depth to change.
If you find the gantry is flexing, fix that first.
You should verify that the machine is adjusted and in proper working order before running these tests.
The PRT is a good machine and will provide you with years of great service. I think ShopBot makes the best kit router package out there.
Ed Lang
PRS Alpha 48
Techno LC4848
Trotec Speedy 300 45W laser
M-300 50W laser
VLS4.60 50W laser
Aspire V3