Specifically it relies on the inotify protocol (see
https://yabb.jriver.com/interact/index.php?topic=96935.msg669539#msg669539), which is supported by modern versions of SMB (the filesharing protocol used by most NAS devices), but not by older versions of SMB.
I don't own a synology device, but googling around it looks like their inotify implementation may be off by default so you may need to tweak a configuration option or two. Media Center automatically runs a scan on watched folders every two hours, so it's especially odd that eight hours can pass without MC seeing a change (unless the NAS is hibernating and MC doesn't wake up drives just to scan them). I have a drive with about 7000 folders on it (probably only 60K files), and auto-import works perfectly and within about 60 seconds, so there's no generic issue with "large drives." The issue is a "MC is not getting inotify events from your NAS for some reason" issue.
You will probably find it most profitable to do some digging about in your NAS's firmware/configuration. Some avenues for exploration:
1) Try to identify any other differences between the drives (filesystem? sleep settings? etc.)
2) Consider if there's any difference about the way you put files on the two drives (i.e. filesystem copy and paste vs. ftp vs. something else). I've seen some reports that ftp uploads don't send inotify events correctly, whereas SMB copying does send them (i.e. copy and paste in explorer).