I have noticed at times that UpdateMedia doesn't seem to scan in some media for a long time, and I actually suspect, at all!
I have just rebuilt my core, but I'm now seeing the same issue again - it definitely scanned in the existing media over time. But I just added a new piece of media (.avi) and it didn't find it after hours. I believe that UpdateMedia sleeps for 2mins if it has nothing to do, and then looks for any directories that have changed and scans them in if needed... right? So it should certainly have gotten the new media quiet quickly. If I manually sync it finds it just fine. In the Sync menu it can see the media on disk, but it has the drive icon indicating that it isn't in the database until I manually sync.
I also noticed some CIFS errors popping up in dmesg, so I tried switching to smbfs but that doesn't seem to have fixed it. I have tried in the past reloading the router, rebooting the system or just unticking the Update Media Daemon box and re-ticking it... all seem to have no impact...