1) When two axis are in motion together, the axis with the lesser distance to travel will run slower than the desired IPM rate. The Axis with the most distance to travel will run at the desired IPM rate. 2) You can create as many "ini" files as you like. They are meant to be a way of useing multiple CNC machines on one PC. They can be useful for other purposes as well, like different setups on a machine. You don't need to delete the default machine ini or any older ini files you created, unless you want to. 3) The latest version of KCam is .26 and the latest MaxStepper firmware is 4.0.3. I don't believe an older version will correct this.
KCam will make determinations as to the max speed a move should be. Some things that effect these decisions are vector changes, distance, max IPMs per axis. It's possible one of these is affecting your rates or possibly a software bug. When cutting a complicated shape, the axis will not go the max speed unless it is a long straight cut where it can ramp down prior to a sharp turn.