This worked for me using ms-access:
1. Open the MDL file using ms-access. (Other threads talk about this and the password).
2. Open the BUTTONTB data base.
3. There is a column that has an id for each key. You will find that duplicate keys have the SAME ID!! It is a number usually between 7 and 35 and usually numbered from left to right and top to bottom of the screen (i.e. 7,9,11,13 on 1st row, 15,17,19,21 on second row, etc.).
4. I don't know how to sort by 2 columns in access so I exported to an excel spreadsheet then sorted by device page and then this "id" column. This instantly shows up all the duplicate keys.
5. In access, you can change this number (Try to keep it odd between 7 and 35, else don't know what would happen). Also open the other databases, and be sure they don't reference this same ID (I don't think they do, but if so you would have to change them too, especially BUTTONTEXTTB).
6. Save the file in access and reopen using the normal software to make sure nothing got corrupted. Download and try relearning to two of the keys. They should now each be able to learn independently.

The physical placement of the keys doesn't seem to necessarily be related to what causes them to be assigned the same id. They can be spread apart and this still happens.