Suggests a pump issue, sticking check valve or piston seal starting to
leak, that is exacerbated at higher pressure when the column is in
place.
Consider the cycling of room air conditioning/heating.
Do the waves that you see when the LC is connected directly to the MS
(no column) correspond to the pump cycles? If so, what kind of pulse
damping does your HPLC use?
See if you can monitor the temperature. If you have it at say 180degC,
it should stay within about 1-2 degrees of that. If it's changing over
4-5 deg, you can get this type of behaviour.
-Steve