When balancing a machine, phase readings should remain relatively stable during the test. Variations of a few degrees are normal, but large jumps or readings that seem to meander around the full 360 degrees are not acceptable. If you have checked your balancing equipment, tachometer and tachometer target and believe that everything is connected and configured properly, then the problem may be that the machine is operating near a resonant frequency. Shut the machine down, attach an accelerometer and perform a bump test to see if any natural frequencies are present near the running speed.
Another possible cause of unstable phase readings is looseness. Check the foundation of the machine for loose bolts or cracks. Run the machine and collect a vibration spectrum. Look for strong 1x harmonics or sub harmonics in the spectrum that would indicate rotating looseness.