FCK editor loads homepage in textarea on a subdomain

Issue Summary

I am using subdomain module to write a few path alias to show us as a subdomain.
After I have upgraded to drupal 6, (FCK editor 6.x-2.0-beta1), there is a strange behaviour. This behaviour did not exist in 5.x.

Whenever I am on a page that has a subdomain in the URL, FCK editor box is filled with a complete replica of the home page.
For example a comment box on http://test.example.com/node/200 is filled with a copy of http://example.com
I was wondering what causes this and how I can stop this from happening.

Other than that the module works flawlessly on other pages.