The cause of the problem is not only interesting and useful, it's a requirement.
Was the paint applied before the sealant had cured? Was primer applied before it was cured? Was it cured totally within temperature parameters or was it too cold at some point that caused the curing to take longer? All these things matter with the long term coating of paintable flexible sealants. We've just sent 5 boxes of a specialist sealant back to Germany as it was out of spec and waaay too thick, like it was out of date, but was well within its "use-by". We had the rep out and he agreed. I'm pretty sure we're not the only customer with a faulty product. At $180 a box, someone won't be happy.
I'm unlucky enough to have to play with this stuff daily. Preparation and curing are hugely important, so to find a solution, you need to know the cause.
Oh, btw, it's not silicone, it's a flexible sealant. Totally different products (try painting silicone) /pet peeve