ok, after a month of dorking around with emby, i've decided it's not for me. glad i tried it, but just too many issues compared to PLEX.
i did finally figure out the problem with emby as to why no movie files were showing up in the library. it turns out, if the file scanner encounters certain conditions (that PLEX handles just fine), it completely aborts everything. in my case, I had a sub-folder with permissions 000, which I had set to exclude a copy of a movie I encoded with some experimental settings and didn't want PLEX to pick up. PLEX would just ignore it and continue on detecting other movie files. emby will completely abort the entire library scan and not even leave a log messages about the issue. i could have 1000 movies and a sub-folder with 000 permissions and it will not scan the other 999 movies. I had to discover this the hard way by adding a movie one by one and trying a rescan until i found the folder that broke it. to work around the issue, i created a separate folder, and symlinked all my movies except for the sub-folder with 000 permissions. and then emby started to populate my movies into the library. however, after finally scanning my movie collection, i found that emby's movie detection algorithm just wasn't as flexible as PLEX; it had a hard time with several movies that I had to manually identify; things like the Star Wars series. Even worse, was that for a select dozen or so movies, it was not able to identify at all, even manually, it would not show an entry for certain obscure movies; yet going to the movie databases I could find the movie meta data. clearly something is wrong with emby. lastly, emby also had a lot of problems with srt subtitles on several occasions. as a some times software developer/ consultant myself, the lack of logging for most of the error conditions above is also really troubling.
the last 2 issues have no work around, so at that point, i decided emby is not for me at this time. i may try it again in a couple of years perhaps. i don't have any gripe with PLEX at this time, but having heard that emby uses a lot less resources, was more responsive during playback interaction, etc., I was hoping it would work better for me and was going to buy a lifetime subscription.