I'm having this same issue.
Tried to replicate the issue by pouring water in various places on roof but can't seem to induce the issue short of waiting for it to rain.
Kinda curious if it's water sliding under via surface tension.
I also noticed that it doesn't always happen on my drivers side ...passenger side is a different deal.



EDIT:
Also, I can drive it around in the rain fine without issue. It's just letting it sit in hard rain that causes it. Light rain causes no issue