We patched everything on our main roof to no avail. Though we only had a small leak (at the head of the bed), we wanted it fixed. We figured it out by keeping our slide closed during a rainstorm. No leaking - it was the slide roof seams. Not much water got under the topper but all of it was ending up in our carpet.
If you can make sure the floor is dry, try closing your slide and flooding that (out)side with water. If none gets in, it is the slide. Alternatively, try flooding the main roof with water. Try particular spots if possible. If the leak returns, there is a leak on the roof. Check all your seals and seams.
Good luck. They can be annoying as hell until you figure it out.
2015 Jeep Willys Wrangler
2014 Fleetwood Bounder 33C
States camped: all but Hawaii
more than 1700 days on the road