OK, time for troubleshooting 101.
Step 1: Measure the mains frequency without the inverter.
Step 2: Take a look at the mains waveform without the inverter.
Steps 3 and 4: Do 1 and 2 with the inverter operating.
Don't apply a solution until you understand the problem.
By the way, I believe the mains frequency is supposed to be between 49.85 and 50.15 Hz, so it may well be that the inverter is actually running out of tolerance and needs to be looked at, rather than fixing the clocks to match the inverter. Without the data, you will never know for sure....
Also, it may not be a "noisy" inverter. The inverter may be outputting a stepped approximation to a sine wave and that is what is causing the issues.