When I loaded the page the first thing I did was highlight that stupid box and kill it with the developer bar. I'm at 1080p and 125% DPI.
As a general rule, anything that can hover over other content on the page (from share buttons to menus and beyond) are going to annoy someone and break someone's experience. No exceptions. If it isn't happening today it will happen tomorrow.
Based on my experience with a portrait-oriented monitor for document editing, nobody bothers making websites work at viewport sizes other than "maximized on the designer's screen."
If you want me to put on my pedantic hat I'd that it's distracting still without the white space provided by 1080p. I really hate being overly picky like this but I want you to get valuable feedback. Ignore it, or take it but I applaud how quickly you fixed the issue to get this.
EDIT: I went back and checked closer and no there are no pixels that I can't see.
I loved Tutum until they became Docker Cloud and started charging per node. The flat monthly price on your product is way more attractive to me.