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There is a registry entry which determines where extensions go. It is dangerous to move installed products. Anyway, you might want to check that the registry was updated with the new paths for extensions.
The Application mover that I used did update the registry for me, I've tried searching my registry but havent found anything yet. Do you have any suggestions on what to search for?
Extension Manager gets the insallation path of all supported products (DW, PS, etc) from the database which is created during the suite installation. Application Mover doesn't know this database and can't update it, so after moving Extension Manager can't find all moved products.
To install extension bypassing Extension Manager, please refer to http://forums.adobe.com/thread/977023?tstart=0. Although this guide is intended for Bridge, it also applies to other products.
Managed to install it, thanks!