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The most robust way to fix is to start afresh, removing Reference Manager/EndNote and then putting it back (with the correct version of the CWYW tools). Note these instructions require re-installing your software, so have your product key (EndNote) or Serial Number (Reference Manager) handy.
Select your software for the appropriate instructions:
EndNote
Reference Manager
EndNote
Please make a back-up of your documents and libraries and then reboot your PC. When it's re-started, please close all programs that open automatically, double-check that Word, Outlook, RefMan are all closed, then perform the following:
If using Windows Vista or 7 (or later), please first turn off User Account Control (UAC). If you're using Windows XP, please skip straight to #1:
Windows Vista:
Start > Control Panel > User Accounts > Turn User Account Control on or off > un-tick the box and press OK.
Windows 7:
Start > Control Panel > User Accounts > Change User Account Control Settings > move the slider to the bottom > press OK.
NOTES:
You will have to reboot your PC after doing this.
You may find some additional steps in the Control Panel if your view is set to 'Category View'. For example, you may have to click on 'Users' then 'User Accounts' then your username.
1. Un-install EndNote via the 'Add or Remove Programs' (Windows XP) or Programs and Features (Windows Vista/7) section of the Control Panel.
2. Download the EndNote installer from here:
EndNote X2
EndNote X3
EndNote X4
3. Hold down the Windows Key and press R to bring up a 'Run' box. It in, type regedit and press OK. You're now looking at the Registry Editor.
NOTE: These instructions are for Word 2010. If you have a previous version of Word, they change accordingly:
For Word 2007 replace the number 14.0 with 12.0
For Word 2003 replace the number 14.0 with 11.0
Navigate to:
HKEY_CURRENT_USER > Software > Microsoft > Office > 14.0 > Word
Right-click on the 'Data' key and select Export. Save it to your desktop as 'WordData-Backup'.
Right-click on the 'Data' key again and select Delete.
Navigate to:
HKEY_CURRENT_USER > Software > ISI ResearchSoft
Right-click on the 'EndNote' key and select Export. Save it to your desktop as 'ENCU-Backup'.
Right-click on the 'EndNote' key again and select Delete.
Navigate to:
HKEY_LOCAL_MACHINE > Software > ISI ResearchSoft
Right-click on the 'EndNote' key and select Export. Save it to your desktop as 'ENLM-Backup'.
Right-click on the 'EndNote' key again and select Delete.
Navigate to:
HKEY_LOCAL MACHINE > Software > Microsoft > Office > Word > Addins (note this location is different to the above)
Right-click on the 'EndNote.WordAddin.Connect' key and select Export. Save it to your desktop as 'ENAddin-Backup'.
Right-click on the 'EndNote.WordAddin.Connect' key again and select Delete.
4. Close the Registry Editor
5. Double-click (XP) or right-click and select 'Run as administrator' (Vista or 7) the installer you downloaded in step 2, and install EndNote with you product key.
6. When the install has finished, start EndNote, open the sample 'Paleo' library, then open a blank Word document. The order here is important.
Try to insert a citation. If this works but you have problems with a specific document, please see here: 
Reference Manager
Please make a back-up of your documents and databases and then reboot your PC. When it's re-started, please close all programs that open automatically, double-check that Word, Outlook, Reference Manager are all closed, then perform the following:
If using Windows Vista or 7 (or later), please first turn off User Account Control (UAC). If you're using Windows XP, please skip straight to #1:
Windows Vista:
Start > Control Panel > User Accounts > Turn User Account Control on or off > un-tick the box and press OK.
Windows 7:
Start > Control Panel > User Accounts > Change User Account Control Settings > move the slider to the bottom > press OK.
NOTES:
You will have to reboot your PC after doing this.
You may find some additional steps in the Control Panel if your view is set to 'Category View'. For example, you may have to click on 'Users' then 'User Accounts' then your username.
1. Un-install Reference Manager via the 'Add or Remove Programs' (Windows XP) or Programs and Features (Windows Vista/7) section of the Control Panel.
2. Download the Reference Manager installer from here
3. Hold down the Windows Key and press R to bring up a 'Run' box. It in, type regedit and press OK. You're now looking at the Registry Editor.
NOTE: These instructions are for Word 2010. If you have a previous version of Word, they change accordingly:
For Word 2007 replace the number 14.0 with 12.0
For Word 2003 replace the number 14.0 with 11.0
Navigate to:
HKEY_CURRENT_USER > Software > Microsoft > Office > 14.0 > Word
Right-click on the 'Data' key and select Export. Save it to your desktop as 'WordData-Backup'.
Right-click on the 'Data' key again and select Delete.
Navigate to:
HKEY_CURRENT_USER > Software > ISI ResearchSoft
Right-click on the 'Reference Manager 12.0' key and select Export. Save it to your desktop as 'RefManCU-Backup'.
Right-click on the 'Reference Manager 12.0' key again and select Delete.
Navigate to:
HKEY_LOCAL_MACHINE > Software > ISI ResearchSoft
Right-click on the 'Reference Manager 12.0' key and select Export. Save it to your desktop as 'RefManLM-Backup'.
Right-click on the 'Reference Manager 12.0' key again and select Delete.
Navigate to:
HKEY_LOCAL MACHINE > Software > Microsoft > Office > Word > Addins (note this location is different to the above)
Right-click on the 'RefMan.WordAddin.Connect' key and select Export. Save it to your desktop as 'RMAddin-Backup'.
Right-click on the 'RefMan.WordAddin.Connect' key again and select Delete.
4. Close the Registry Editor
5. Double-click (XP) or right-click and select 'Run as administrator' (Vista or 7) the installer you downloaded in step 2, and install Reference Manager with your serial number.
6. When the install has finished, start Reference Manager, open the sample database, then open a blank Word document. The order here is important.
Try to insert a citation. If this works but you have problems with a specific document, please see here: 
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