Skewed holes can be caused by all of the things suggested, you need to look at the consistency of the bad shapes, if it is all over the sheet, and on various parts, and the flat spots are on different sides of the circles, then you need to look at the parts moving inside of the sheet or the...
You should be shoot the power puc directly out of the resonator and depending on what size puc you have and the calibration you should receive the exact wattage of the laser. 2200 watts. If the wattage is very low, then you internal mirrors inside the resonator probably need to be cleaned or...