1. Turn on "reading mode" from tray menu
2. Open preferences window
3. Change microbreak timer (you can change it up and down to the same value)
4. Click close
5. Do not move mouse for a few seconds - reading mode is not active now, lack of input movement will count as microbreak.

The same behavior after rest break:

1. Turn on "reading mode" from tray menu
2. Perform rest break
3. Do not move mouse for a few seconds - reading mode is not active now, lack
of input movement will count as microbreak.

Thanks. The latest snapshot should fix this problem: 

http://snapshots.workrave.org/20110209/workrave-win32-v1_9_3-41-g831c769c01-20110209-installer.exe

Note: After a microbreak all timers are automatically restarted, even if you do not use keyboard/mouse.  However, after a restbreak all timers are halted until you use keyboard/mouse again.