Or rather following the methods described here http://forum.kalypsomedia.com/showthread.php?tid=10399, I'm still unable to get the game to play my custom music selection other then the contents of the first thirteen of my tracks.

Is there by any chance something in the recent modern times expansion that disables this functionality or is there perhaps anything in the hidden windows folders disabling this functionality that I'm not aware of?

There is.

Expansion.hpk lateloads (so people can't just copy and paste it into their directory). This means it clobbers existing data, and breaks almost every mod.

I don't suppose there's anything we can do about that is there?
I hate it when companies get this hostile to mods because they're hoping to sell us some dlc.
In any case, while the in game music isn't that bad, the severely limited amount of tracks does get boring rather fast and having to run a third party program in the background is also something I find to be rather annoying, so Kalypso guys in case you are reading this please consider fixing the custom music issue in an upcoming patch, unless of course you're planning on selling us something like a rebel radio dlc with different anti government announcers who play our custom mp3 files.

They didn't get hostile, the DLC loading process didn't change, it's just that nobody in the community accounted for the clobbering of old data.

Getting around it thus far has been tricky ... at least in a way which is safe for me to release without Kalypso wanting to take away the toys I've got now

I actually found a way to mod the game better than I was before, but it's taking some time to put together because I just don't have the time.

For the music modding, I think that was Snake's brainchild originally, and overloading fails here because it gets clobbered.

For this, try putting the file here: ex\Game\Sound\Playlists\Playlists.lua

That's what Modern Times should be loading.