Any time you open the preferences dialog, the Workrave window goes away (even when you are supposed to take a break).

Moreover, if you keep the preferences dialog open, in order to "cheat", you just need to bring it to the front (Windows: ALT+TAB), and then come back to the previous program (ALT+TAB again).

This is so by design. The idea is that if you mistype in the preferences dialog, it could be that you are forced to take a (possibly very long) break immediately. If you don't have skip/postpone enabled, you could be locked out of your computer for a very long time. Hence, you will not be prompted for breaks when the preferences dialog has focus.

If you really wanted to "cheat", you could, instead of opening preferences, select "quiet" or "suspended" from the "mode" menu. That, too, will stop breaks from coming, without you needing to switch to the preferences dialog in time. Hey, workrave even remembers the mode when you stop and (re)start it :-)

This is indeed by design. Workrave switches to 'quiet' mode when the preferences window is open and has the focus. Workrave will still count your activity. So you will be prompted to take a break if some other window is focussed.