This all stems from having issues with the background service not running suddenly in 1.x on a WHS2011 install. I couldn't get drivepool to run and all of the pooled folders were showing up empty. I saw that there was a new 2.x version when I went to download an update hoping that would solve my problem. Anyway, I went ahead and removed 1.x and installed the new 2.x. Drivepool is now working but I have a few folders that aren't in the pool and are empty. Drivepool is still "checking" @ 16.3% so could it be something with that? I find it unlikely though since other folders are showing correctly.
Under server folders, the ones that are filled with data are correctly showing under the pool drive "I", whereas the ones that aren't working are under "K". However, "K" is actually one of the actual drives mapping designation and is being shown as a part of pool "I".
Hopefully this all makes sense and there's is an easy fix. There are some screen shots attached for reference.