I’ve been dealing with incorrectly installed windows in my house. The house is stucco, and the building paper which provides the water proofing was cut back when the windows were installed, so water leaks through the gap between the window and the building paper. The issue is under the surface so it was hard to track down until we took off the trim surrounding the window. In our case the fix was to remove the trim then cut out stucco if needed until we reached the existing building paper, then tick Moiststop under the building paper and over the window flanges. This fixed the issue.

I’m not familiar with wood siding as a water proofing system, so things may be different for you. If it relies on a moisture barrier that’s under the siding, the leak could be coming from that. I’d start by removing the trim to see if you can see issues with the waterproofing under there. If you can’t, you could cut back the siding further until you can fit the PVC window flanges in such a way that you can properly water proof it, then re trim the window and you’re good to go.

Not sure if that helps, but we drove ourselves crazy trying figure out why our windows were leaking.