When I open up Lightroom 6 there appears to be two message/window screens that appear for a very brief moment. I can't find these pop-up windows once the program opens. Is there a trick to seeing what these are? They may be causing a startup issue on occasion so I am wondering if there are questions that need to be answered. Thanks.
If you don't see that error message before it disappear, then there's no way to find the message.
You can turn off the Graphics Processor from the Lightroom preferences and check if you still get some popups on the startup.
Go to Lightroom Preferences from the Edit menu
Click on Performance tab
Uncheck the Graphics Processor