Basically for this behavior to occur, most common problem is setting DPI of the monitor to be 100%, which you say you already configured according to this article (http://docs.telerik.com/teststudio/troubleshooting-guide/recording-problems-tg/highlighting-misaligned).
Next thing is to ensure your browser is calibrated and its zoom level is set to 100% (http://docs.telerik.com/teststudio/features/project-settings/browsers)
This can also happen if you have multiple monitors (as is your case) and different monitors have different settings - can you double check that? And see how you exactly configure multiple monitors - extend displays or clone, or any other option? You can try different monitor configuration options just to see if this fixes the problem.
In specific cases this can also happen if you are using a 4K monitor or if this is something specific to your website implementation. If the case is the latter, can you provide us with sample page and access rights to where you experience the problem, so we can investigate on our site?
Last thing is to check if this is Chrome specific problem and try using Internet Explorer/Firefox for recording to see if behavior is observed there also.
Thank you for your feedback and cooperation,