Having the same problem...here are my answers to your questions:
Are you using DM on a PC or a Mac? 6.1 on a PC
If a PC, what version of Windows are you using? XP Pro SP3
What BlackBerry device do you have? Storm 9530
What BlackBerry OS are you using? 5.0
What are you trying to do when the Apply button does not work? In the applications menu, when trying to add/remove applications as well as receive the update for OS 5.0 that it tells me is available, the apply button seems completely dead. When I hover the mouse over it, it doesn't highlight like the other buttons in the window do and nothing happens when I click it. All the other buttons seem to work.