Instances do not match item count...

[simbun]

Is the Synology simply a sync from the Mac, if so, what does your sync software report?

I'd be tempted to produce a log using writeAllTags for each instance and diff the two.

If your mac instance is looking at a mac source, can you create a new profile and point it to your Synology content directory? That would rule out any software differences.

If both MinimServer's are pointing to the same data, how many items/albums are reported when you select Pat Metheny from the Artist/Album Artist index?
If both are pointing to the Synology for their music files, could it be a permissions problem (although this would likely cause MinimServer to write messages to the log during scanning); although given both have the same album counts it would have to be something like a backup/recyclebin. You could double check the groups/permissions that MinimServer and the mac shared user have. Alternatively, sudo to both users and do file counts, something like 'find . -name "*.flac" | wc -l'.

There's not a lot to go on, so just a few thoughts.