Notice: this information was written when Microthemer version 2 was current. On Dec 26th, 2014 version 3 was released with a completely new interface. Some of the information may be redundant, but as much of
the functionality remains the same in version 3 we haven't deleted this post.
Ok, it took me a while to figure this out. But I can see when I click the “css” link under view site that Microthemer is adding position:relative whenever I apply CSS3 styles to a selector. This messes up my web page layout a bit.
In short, you just explicitly set the Position of the selector in question to static (from the dropdown menu) or set CSS3 PIE to “off”. But the reason Microthemer adds this automatically, when CSS3 PIE is “On”, is that position:relative or position:absolute is an often needed hack to make CSS3 PIE work properly.