I use BIS.. but I don't think the issue at hand has anything to do with BIS or BES.. The issue I was having was that I could use the other applications on the Desktop Manager fine, but the Applicator Loader would tell me no BlackBerry device connected. The solution? Installing the OS Device software. It's rather confusing because the "device software" isn't for your handheld device, it's for your Windows environment and Desktop Manager.
Go here: BlackBerry - BlackBerry Desktop and Device Software Download Sites
and select your carrier and the device software. Install and you should be good.