Is the target for templates defined in the Copies & Folder section of Tools/Account Settings the same as the "templates" folder in the Folder Pane? If the target is Templates on the IMAP server, check that that folder is subscribed (right-click account, Subscribe...).

Both of those are fine, the right folder is set up in the account and the folder is subscribe to in the IMAP server. Still the templates do not appear anywhere, when I save them they just go into the ether

Try setting the target folder to Templates on Local Folders.

It seems to work in local folders, I may have to uninstall and do a clean reinstall, this has been updated many times but a fresh reinstall may solve it, will let you know and mark is as solved if it fixes the issue

A clean reinstall won't do any harm, but you're more likely to achieve a clean start with a new profile: Help/Troubleshooting, about:profiles, to create and run profiles. If the new profile works properly, mail, contacts etc. can be transferred from the old profile to the new.

so once I create the new profile I can then copy the imap and local directories to the new profile? I see the files and the matching ones with msf extents so can I assume both are to be copied to the new location?

Also, how does one switch between profiles?

When the IMAP accounts are added to the new profile, the folders will download from the IMAP server. For local mail, copy the mbox files - the large files with no extension, named after folders - to Mail\Local Folders in the new profile, with TB closed. Ignore the msf files, they will be automatically recreated.

Launch a different profile from about:profiles; multiple profiles can be open at the same time.