Rex. What TC version are you using. - note- below is just a guess as I haven't seen the pop-up you mentioned.
That pop-up sounds sound strange, at first I thought it was the pop-up notification - quote by IMSI from another thread "We have added pop-up notification to all TC builds which contain our auto-update technology 2016, 2015, 21 and 20. This allows us to notify all TC users about current news, special offers and new products from within the application". which I believe can be disable by clicking 'don't show again'. However for v20 (if your still using v20 deluxe), there won't have been any new features, nor updates unless your version had not been updated for a few years.
It may just need your workspace resetting, if you could let us know the version (help menu - about TC), is it just the offset or has the whole menu setup changed, under options menu - native draw, do you work in GDI or RedSDK, (and has it changed from what you used), if it doesn't sound like the above - do you have a screenshot of the notification.
To reset workspace - Tools menu - customise - drop down the box below 'load from' choose you own custom one if you have previously saved it, else choose one available, click load from - if the box starts flashes, click on the windows taskbar should stop it (it does for me), if it doesn't look right choose another one, if you hadn't previously saved your own workspace, you will need to change things to your own liking.
For GDI mode - options menu - Native draw - select GDI mode (unless you are used to using RedSDK)