This is closely related to issue 876. (Therefore I gave it the same severity and priority). The work around in issue 876 (change registry to lowlevel monitor) works fine for me.  This issue is filed for your information.

I see the same behavior -- the break dialogs never come down, apparently because WorkRave thinks there is mouse/keyboard activity. In my case the problem is due to USB keypad I use.

The product I have is an X-keys SE, it is described at http://www.x-keys.com/xkeys/xkdesk.php.  There it is called "X-keys Desktop USB" but I think my model may be a bit different than the newest one.

OS is Windows 7, 64-bit, all current updates applied.

I am also running MacroWorks3 version 1.0.1.7. This program comes with the X-keys product and configures the keys to execute various events.

Something about  the X-Keys and/or MacroWorks3 causes WorkRave to believe there is constant mouse or keyboard activity.  After a period of activity WorkRave brings up a dialog to remind the user to take a break.  If activity stops the dialog will be taken down after the configured amount of time has passed.  But the dialog will never go down because of some interaction between the device and the two programs.

As I said at the beginning, I have changed my registry as follows: 
[HKEY_CURRENT_USER\Software\Workrave\advanced]
"monitor"="lowlevel"

Everything is now working fine.

Thank you for a great program!

I forgot to mention that I have reported this to PI Engineering via their support email address.

Thanks for your feedback! Workrave 1.9.3 uses the lowlevel monitor by default. I got several reports that this fixes the timer-keep-running problems.