When I start BTC Core through the shortcut(with that special target) it goes through veryfing blocks but it won't open the BTC Core because it says not responding and the only thing I can do is to close it. The last time it was up and running the procces was at 75% or so if that helps.
BTC Core can be quite CPU intensive... and it can do the "not responding" thing occasionally if it is really busy hashing stuff while calculating checksums etc... any chance you can post the debug.log
When I start my first BTC Core without that shortcut, it opens normal and is fully synced but that doesn't help me since my Armory balance doesn't change with that one.
In that case, with your first BTC Core open (and fully synced)... can you goto: "Help -> Debug Window" and see what the "Datadir" path is... if that is NOT "D:\Bitcoin" then you can try and set the path in Armory to be whatever it says there...