The latest release of Madsonic gives you several options that I would recommend you try first.
In the latest beta, Version 4.8.3306.beta3, here are the options:
Show albums year
Show albums year in REST-API (Apps)
Sort albums by foldernames
Sort MediaFile Folder Selector
Sort files by filenames
I'm actually a bit too simple-minded to understand exactly what you're up against with your particular storage strategy, but I would think that if things worked fine for you in ver 4.6, then using the option to sort by foldernames might work for you. There's also some flexibility and customization associated with using the sort MediaFile Folder Selector that can probably address your particular issue, as it was more complex than I was interested into getting into deciphering exactly what it was doing.
Perhaps if you send a msg directly to MadEvil he can sort it all out for you.
HTH
EDIT: I think this may be relevant, but again I never took the time to figure out what was going on, but you may be able to look at it and make sense out of it. If you do, maybe you can explain it to me.
viewtopic.php?f=15&t=10445&start=0The post is towards the bottom of the page.