The proper reference phase is crucial to achieve critical coupling. Follow the above procedure to retune the cavity properly. Condensation in the cryostat . Water is a huge microwave absorber. If you are running a low temperature experiment, make sure that you have purged the cavity with dry nitrogen to minimize water losses.
Water absorption can also be a problem on humid days.
When Everything Else Seems OK Check all of the cables. Check both the modulation and the preamplifier cables. Even if these look OK remove and reseat them. Check the sample position. Verify that the sample is well centered in the cavity.