So the thing that would be easiest for me is if I could reproduce your problem here. Would you be able to send me a copy of all of the HTTPS certificates in the chain? This will enable me to create a very similar certificate chain here, and easily debug the issue.
The following instructions will let you save the HTTPS certificate chain from Firefox 3.6.3, but hopefully they should be fairly similar for other versions:
1. Connect to the relevant server, e.g. by putting https://server/
in the address bar, and pressing enter.
2. After the page has loaded, right-click somewhere on the page.
3. Left-click the View Page Info menu item.
4. Left-click the Security tab.
5. Left-click the View Certificate button.
6. Left-click the Details tab.
7. For each one of the certificates in the Certificate Hierarchy, left-click on it to select it, and then click the Export button; the default file name should be fine, so just click the Save button.
You should now have several files, one for each one of the certificates in the Certificate Hierarchy.
If you could email me all of the files, firstname.lastname@example.org
, that would be awesome :)