How I solved it ..... for now!
Not an elegant solution and possibly only temporary, but I SSH'd into the NAS, opened the "/volume1/video/Movies" directory and chown'd every file/folder recursively to be owned by "me" and have group "users".
Once I went back into Emby I ran a 'Scan Library Files' on the "Movies" library and it found every movie. Its still getting the images etc. now so I'll examine the movies it found in the library and compare with the actual directory, but the new movies that came within the last couple of days have been found now.
What i would like to know is, is this an Emby issue with Synology? Or the other way arround a Synology issue with Emby.
The reason why i ask is this might need to be taken up with Synology then?