What paint should I use over decorator's caulk so that it matches the surrounding area?
The caulk mentioned in your comment appears to be a typical latex "painters caulk". It should accept paint just fine, with no bleed-through. I'm not sure what's happening in your case. 

I'd get a quart of a high-grade primer such as a Zinsser product. There are plenty of good ones. Cover just the caulk and blend into the wall. Let that dry well and try your topcoat again. 

If you painted over the caulk entirely you may need to use a paint remover to clean that up first.