It might be the way hardware is detected or the video drivers are selected. It might change from one boot to another. Just a thought. I would try using some of the cheatcodes to specify the video parameters while booting. Selecting the drivers, etc might give you a solution. There is a list of cheatcodes and some explanations located under the "Documentation" link at the top of the page. Another one you might try is noddc. I'm not sure if it's listed, but it has solved a few monitor issues for me in the past.