All of a sudden my wind vane is off 90°. I took it off the mount, put on the workbench, and aligned the way the manual tells and I'm still off 90°. The one thing I noticed on the bench with the vane removed my the flat spot of my shaft doesn't come true to the right. It's off a few degrees. Would that make any difference?
Assuming the 90° difference is constant, you can check the console and make sure an offset wasn't somehow added accidentally, and if it wasn't, then you can add an offset to correct the reading.
As long as you followed the manual when you had the anemometer down, I'm not sure what else you can check for. I think it's possible the shaft could have gotten off, but if it's reading 90° off, then it seems to me the shaft would also have to be 90° off and not just a few degrees, but I guess maybe it could be a symptom of something else being loose.
In any case I think I would adjust the offset and see if it sticks.
If you have a clear night, you can also look for Polaris, the North Star. If it's 90° off and in the east or the west, you have a whole 'nother problem.