I have a base soft top. This issue has been discussed in several threads. Normally, the top isvvsealed up nicely with little noise and no leakage. But, with a very strong sidewind, it can happen.
I have a base soft top, too. I am at highway speeds on a daily basis (70+ mph) and today we had winds at 20+ mph in addition to that. I've never seen that happen, ever. Have you had it to the dealership to look at? Even when we had recent gusts up to 50 that wasn't happening.