Cannot delete site columns even after removing all references

Hi

We currently have a SharePoint 2010 SP1 setup in our environments and are having a problem in removing a couple of site columns that were added in by a third party product. Despite best efforts this has not been possible and we are hoping to get some advice around this.

Here's a brief overview of the issue:

1. We have two Site level columns that we are trying to delete, at the root site level. But when we try to delete them, we get the message (“Site columns which are included in content types cannot be deleted. Remove all references to this site column prior to deleting it”).
2. We have run powershell scripts to ensure that these columns are not part of any List, Web or Content Type in the entire site structure and have also cleaned out the recycle bin (site and admin bin) to try and remove any existing references. We have also ensured that these columns are not marked as hidden, read-only, or sealed.
3. We have also tried deleting this through SharePoint Manager but get the same result.
4. The only possible explanation seems to be that there must be orphaned references in the database. (we have seen references to similar cases elsewhere and indeed we are seeing some entries in the DB for these fields, that are not visible in the UI or when querying through PowerShell). However for obvious reasons, we do not want to modify the SP database !

Any advice on how to track such missing references, or what can be done to delete a column in such a case, would be much appreciated !

Do let me know if you need any further details.

Thanks
Rob