On line 2500 of ext-all.css is "x-grid3-hd-checker", which overrides a larger CSS entry on line 2484. The entry on line 2484 already positions the checkbox icon correctly. The entry on line 2500 moves it 1px lower, which is unnecessary at best, "too low" at worst (I actually think the entry on line 2484 should use "2px 1px").
Normally, I would have done all you said, but this is just a report of what appears to be "extraneous" CSS (just search for the class name). There are no visual issues, I just happened to find this while I was ferreting out some related CSS in FB.