I think this is the old two-monitor problem - it's just that Monarch's main grey window is in front of the filter dialog. If you hold down ALT and press space, this will prompt the active window (the filter dialog) to open its properties, and then if you click on M to select the move command (it will all still be invisible at this point) and use the arrow keys to move the window around, hopefully you'll see it re-appear.
Sometimes the filter window cannot be selected using the above mention. I use dual monitors and have experienced the issue for years but the dual monitor problem only exists when connecting via a single monitor and the filter window is left on the 2nd(non-visible) monitor.
If this is not affected by the dual monitors, I would suggest just hitting the ESC button. Keep in mind, if you have an open filter it will not be saved when ESC is hit.