I just did a completely fresh install of MyBB 1.6.11 (no plugins) on a server and posting a new thread in Firefox looks fine, but knowing 50% of users will be using IE, I tried the same thing in IE9 and the "Your Message" box looks a little strange. Screenshot attached.
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It looks like the "Justify text" button is just slightly too wide in IE so it moves down, which then bumps the textarea down to cover the "Post Options" checkbox.
It's not your theme, or your install. This occurs randomly for me in both Chrome and Internet Explorer, on all MyBB sites. My screen resolution is 1920x1080. A quick solution would be adding padding above the check box icons.
I finally got some time to look into this and a related issue with the forums not being able to be viewed properly at 600px wide. It appears to be caused by two textareas and some really bad styling practices. As a result, the hardcoded width and height will cause problems under any browser depending heavily on how fast some parts of the page load. When I tried removing the hardcoded widths and heights using Firebug, it took forever to get just that box to look relatively correct (toolbars and icons, however, still needed some work). However, once I got done, it looked somewhat possible, which is a start, but it really needs a MyBB dev to hammer away at this problem.
The real solution is to completely scrap the current method of how new posts and replies are done and redo them so they look good at a wide variety of screen sizes - including mobile devices. "No hardcoded pixel widths or heights" would probably become a natural part of that transformation, which would, in turn, fix this issue naturally and everyone would simultaneously benefit from a good mobile-friendly-ish theme.