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Almost without question, you have unstable cables. To verify the stabilty of the VNA, do a 1 port calibration directly on the hard-port (physical test port) of the VNA, with no cables of course, and put a short or open from a calkit (don't just leave it open, the radiation is unstable in S11). Put Data->mem and data/mem on S11 and S22. Leave it overnite and see if there is any change. If there is no change, it really is probably the cable.
To test the cable: Place the cable on one port of the VNA, set a short or open from a calkit on the other end. Don't cal. Just do data->mem and data-mem (that's right, data -minus- memory). Look at the result in dB. Immediately after the cal, the trace should show -70 or -80 dB return loss. Now flex the cable back and forth and up and down. The trace for a "GOOD" cable should be -50 dB; if the highest spot on the trace is above -30 dB it is a "BAD" cable: take a wire cutter and immediately cut the cable in 20. For me, I would not use a cable that is worse than -40 dB.
IF the cables are good, and the VNA is stable: the last place to look is at the VNA-to-cable connectors. If this comes loose and then the operator re-tightens it, or if it is not tight at the start, it can cause this kind of trouble.
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