The fact that you say it does it at the same rpm in 2nd gear as it does in third tells me it may be more rpm related rather than speed related. The driveline is going to be rotating at a different rpm in each gear. Is it a half frequency? I don't know but what I do know is you may have several issues since this is not an oem configuration.

You also say it didn't do this before. Is it possible you just didn't notice it before? If not then something has changed. The driveshaft length didn't change, the output bushing didn't suddenly change nor did the driveshaft balance unless it lost a weight.

This is how you need to approach it. What could have possibly changed.