Regarding this item from the RC notes,
|1175662, 1146091, 1152095, 1146363|
Resolved issue regarding the Select All Applications link on Manage Applications page not performing as expected for Unmanage/Remanage actions. Unmanaging/Remanaging a group of applications results in all applications being unmanaged/remanaged.
Has anyone tested if the same problem was resolved on the manage nodes screen as well? As an example, if you filter against something on the Group By box to the left and hit select all it has a little caption next to it that shows the correct number of nodes and asks something to the effect of "do you want to select all 500 of these nodes" but instead of selecting the filtered set it just selects all of the nodes.
I just tested this in my own lab and manage nodes is not working as you describe, but rather as you were hoping.