There might be numerous reasons. Analysing pressure profiles between runs can give some hints. Use Agilent - HPLC Advisor as a starting point for your troubleshooting.
Maybe a bit more detail would help to get you an answer. Here's a few questions:
Is the method gradient or isocratic
Do you prepare the mobile phase freshly each day
Is the column maintained at a set temperature using a column oven/thermostat
Is there just variability day-to-day, or is there the same variability across the day
Provide us more details about the HPLC - what modules does the system contain; I can tell that you have a quaternary pump, since you mention changing the MCGV
Have you carried out any tests on the pump, either leak rate test or gradient test?
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