I was not saying the MainWP is causing the problem and was only pointing out something that has the possibility of being involved in the equation. It should be considered and eliminated as a cause since it does do things related to checking for plugin updates. You should actually deactivate all of your plugins except for BPS Pro and then use the BPS Pro Manual Upgrade Check link / Plugin Update Check Pro-Tool and see what happens to find out if the issue/problem is being caused by another plugin that you have installed on this site.
Another possibility could be that if you are caching your wp-admin area then it is possible that that is causing this issue/problem. The wp-admin area should never be cached for any reason. So you want to ensure that wp-admin caching is not being done on this site.