When you connect to a machine and run a program, it can sometimes pop a windows asking for Y/N or some user input, but I can't see that windows when viewing remote. It appears the program is locked-up but really it's just waiting for input. Have you seen this before and if so, how do you work around it?
You probably should enable the "Capture alpha-blending windows" in the connection properties. Right-click on the connection in your address book, click Properties -> Additional properties and tick the "Capture alpha-blending windows" check box.
Alpha-blending windows are semi-transparent windows and menus.