BitcoinCore does find the blockchain in its custom location, but obviously Armor does not. I don't know why.
Because you have Bitcoin Core setup with it's
data directory in a "custom" location... and have not told Armory (correctly) where that location is.
Can you please start Bitcoin Core, goto: "Help -> Debug Window -> Information" and tell us what the value of "Datadir" is:
That is the ACTUAL data directory that your instance of Bitcoin Core is currently using and is the path that needs to be added to your armoryqt.conf file
Also, I noticed that you have mentioned that you're using the "portable" version of both Armory and Bitcoin Core... however, they are not really "portable" (as they don't create data directories in the location they are run from)... instead they are probably better considered to be "standalone". They don't use an installer etc and you can just put them anywhere and run them, but due to the way these applications work, they will setup their data directories in "default" locations... like C:\Users\USERNAME\AppData\Roaming\Bitcoin and C:\Users\USERNAME\AppData\Armory, unless otherwise specified. I suspect this might be causing some issues with getting your .conf file read by Armory.