Andrew, you are not the only one frustrated by this. It would seem to me to be a real usability oversight by the Quickbooks team and something they should fix in an update. 

Moving the alert box from my main monitor to the monitor displaying QB, then exiting, does not seem to change the location of the alert box on future appearances. So it was worth a try.

Quickbooks development, if you are listening, please fix this bug - it is very frustrating! There are times I sit there waiting for something to happen, thinking that QB has frozen, only to remember to look at my main monitor for an alert. Very frustrating!