We noticed gaps in the borders for some of our controls while using the RoundedCorners Extender. This was a big headache since it seemed to work fine on some pages. I have included a sample image below.
We finally figured out that on the pages where it was not working, we were injecting some diagnostic information into our html as comments. Since this was being inserted before the doctype, it was sending IE into quirks mode and that was causing the trouble. Updating the code to insert comments after Doctype declaration fixed the issue.
Hope this helps somebody out there:).