I read a saying about CNC machines when I was looking at which one to buy. It goes like this:
Time, value and quality. Pick any two of those.
I am using a CNC6040, which is a decent sized machine and works really well for a variety of tasks... but because it is an entry level machine (even at $2000...), it does have some drawbacks. One of them is time. It will take longer to complete some tasks than more expensive, higher quality machines. I can't cut PCB's of excellent quality at 800mm per minute on my machine. At 800mm per minute it will snap bits and generate runout on the spindle. I usually run it at around 450mm per minute, but then again my spindle has a maximum RPM of 9000, not 28000 like yours. Your spindle could be shuttering and vibrating because your feedrate is too fast. It might be moving the spindle faster than the endmill can cut the copper.
My suggestion to reduce the feedrate right down is to determine what the best feedrate for your machine is when cutting PCB's. Start slow (like 100mm per minute) then increase it gradually as it is cutting. Keep increasing it gradually (maybe by 10% each minute) to the point where the machine is cutting nice clean traces quickly. If the machine starts shuttering, or the endmill snaps, or you get run out where your 90degree turns look like larger arcs, you have increased the feedrate too far.
The machine you are using, the material you are cutting, the speed of the spindle and the type of endmill you are using will all alter the required feedrate. Using a 0.1mm V bit will probably require some slight changes to the feedrate compared to an 0.4mm ballnose bit for example. It is all about experimentation.
Once you determine the best feedrate for the task, you can alter the settings in pcb-gcode in eagle for both the feedrate and plunge rate (how quickly the z-axis moves). Set the feedrate to your optimal setting. The plunge rate is usually best set to 20%-30% of your feed rate.
Trial and error my good man. Its all about trial and error.