I have a problem with both column and row headers being rendered what looks like twice!
I'm using an app called Hype (link). Everything else works ok (seemingly) except for headers. I've reported the issue on Hype forums (here) where those who are familiar with the Hype product can download my test document.
All help appreciated.
We need the actual fiddle with your Handsontable instance. This doesn't help us much. I can guess at the issue, it's the "clone" instance of the table which gets rendered on top of the actual table to allow for freezing of panes.
You're probably modifying the CSS on only one of these, making the second one go out of whack. The solution is to either modify them both or to use Handsontable methods to modify the table.