I had the same issue: Emby not scanning my "Movies" library but working fine on the "TV" library.
I'm running Emby 220.127.116.11 on a Synology DS414.
I noticed just a couple of days ago that new movies were not being found. Everything was working fine up until then, TV shows and movies showing up just fine.
I managed to solve the problem for now, but I have no idea what, if anything, was changed to cause the issue to start. I did update the Emby software to 18.104.22.168 - the NAS shows 15/04/20 on the package page which is I think the date of the update. The last movies that were found before the problems started were put on the NAS on around 05/04/20. The movies that weren't found came in around 16/04/20. I have no idea if there's a link to the 22.214.171.124 version or if its coincidence.
During my troubleshooting I tried many times to 'Scan Library Files' just on the Movies folder (no joy), the TV folder (standard counter counting to 100% and finding shows as expected) and a Scan initiated for all libraries together (TV worked as before, nothing on Movies)
I have a USB drive attached to the NAS as an extra archiving drive and I have "Archived" TV shows and Movies on it. I added a new library "Archived Movies" in Emby and it scanned everything as normal. Still wouldn't do the "Movies" library though. I read a post (can't remember where) suggesting that there may be a corrupt folder there, but if there is I couldn't find it.
I guessed it was some kind of permissions problem.
The user "embysvr" is a member of "users" only - I have done nothing special with the permissions since setting up the software initially.
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.
If any of this information is of any use then great. Otherwise, good luck.