Pretty much says it in the subject. Thanks :)

In particular blacken y=1080 on monitor 2, or even more lines on the bottom of that screen. Just a naggy thing happening where a certain full screen browser flash player doesn't actually fill the whole screen, wouldn't be noticeable if transparency and wallpapers weren't on though.

Fixed, had to disable and re-enable the monitor after decreasing the y by one in Monitor Configuration > Splits and Paddings > Height and then clicking Auto-Fill Split. I won't delete the thread just in case someone needs to figure this out too.