As a previous owner of an older 924 and 944, here are some of the problems which were a constant headache. I am not sure if a more modern Boxster could have the same problems which is why I am interested if yours has had any new paint you know of.
Both the old ones had paint that faded to white on the bonnet and roof very easily. The one that did a similar thing was the 924. When I had it it was 20 years old and red. The paint was obviously not original, it was too good, but it would fade. The only way back was a 6 monthly routine with Zymol HD cleanse which removed the old polish, probably the same as claying. Thaen a lot of time with Tcut. Finally a good wax with Zymol. Zymol is an excellent sealer but the first drop of rain and there were white marks on a warm bonnet. Of course the bonnet got warmer because the engine was under it, unlike the Boxster. The 944 did the same but raindrops had no effect. Now a Zymol sealed Boxster is fine.
All I can think is you have a chemical reaction with either the wax, paint, or both. Clean down a small area of the bonnet with heavy clay and see if the naked paint does the same. If it's OK then clay the car and use a different sealer. If the clayed paint still gets the marks then it might be worth trying a paint restorer, probably not as harsh as Tcut, on the same small area and see if the problem is still in the paint.
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