Thank you for taking the time to try my suggestion, the information you provide is very important. Generally, with SP2 we introduced a new way, a Prometheus control registers its css to the page in order to accommodate a common AJAX scenario.
Up until the current build all Prometheus controls would not load their skin properly if they were loaded on the page as a result of an AJAX call - that is, if they were not visible on the client-side when the page was first loaded, and then were added through AJAX. It is likely that this is what is causing the problem, but it is very strange how it happens, as we are not able to reproduce it in our tests. That is why, it would be very highly appreciated, if you could find the time to prepare and send us a test project.
Apart from that, we have another suggestion you could try and that is, to register the tooltip skin css manually. Please refer to our online documentation
for information how you can do this.
All the best,
the Telerik team