This happen on a screen refresh, a reboot will make it go a way and it will return any time the screen is refreshed or monitor is turned off and back on also. It really makes it hard to use the app. I am a reseller and Tier 3 service tech and we are going to drop the software at my shop because it has been know over a year and not been addressed.
Given Start11 was released under a year ago and taskbar support was released initially in March in beta that would be somewhat unexpected 
We were able to reproduce an issue caused by elevated apps sometimes causing the wrong popup to show, but this is addressed in 1.26.
So far we have not been able to reproduce any issue with the wrong popup showing after screen changes.
Are you able to provide any additional information such as what you mean by any time the screen is refreshed? Also does screen scaling get adjusted or primary monitor being changed?
We would love to be able to resolve this for you, but as it isn't something we can readily reproduce we need some help from those who have the problem.
It is also worth noting that we have become aware of a lot of people do not read the messages that popup during first install of Start11 and then set the taskbar to enable the enhanced Start11 features only to then set it to combine mode. If you are using combine mode you probably do not want to enable the enhanced Start11 features of the taskbar given the main one is the uncombine option.
Because of this we have stopped prompting users about the feature and leave it up to users to enable if they wish. Without that on you certainly will not have this problem (or if you do it isn't us)