Hi there,
I've tried manually upgrading Magento from 1.7 to 1.9.1 by following the steps I found on StackExchange (shown below). This included moving all of the /app/etc/modules and /app/code/community etc.. and using a replica of the existing database (running the installer on the existing database to update it) - however NO custom extensions are showing as installed or working on the site. When I go to the Magento Connect Manager there are no community modules installed. Does anyone know if I'm missing a step here??
These are the upgrade instructions I followed:
- Take a backup of current database and current 1.7 code. place maintenance.flag file inside 1.7 code folder to put website offline.
- Download latest magento from the http://www.magentocommerce.com/download
- Remove all folders and files from your 1.7 code except maintenance.flag (but you should have backup somewhere) and place all folders and files from the 1.9.
- Now from your 1.7 merge your following custom folders into the 1.9
- Community app/code/community
- Local app/code/local
- Media
- your theme or package (app/design/frontend/default/<your theme> or app/design/frontend/<your package>)
- custom folders from Skin (both for adminhtml and frontend).
- copy your custom xml files from app/etc/modules/ to current app/etc/modules/
- any custom admin theme folder from adminhtml/default/yourtheme.
- copy your custom folders from adminhtml/default/default/ (1.7) to adminhtml/default/default/ (1.9).
- custom js files if any from app/js/.
- Now go to app/etc/local.xml.Edit database details their.put your database username and password and database name.
- Remove maintenance.flag file and check the site in the browser. it is done.
Thankyou 
Does anyone have any ideas on this please - specifically why the extensions haven't transferred over and how you're supposed to upgrade with respect to extensions?
Many thanks