Set Pixel Rounding to 'Yes', sampling to 'Point', and fullscreen mode to 'letterbox integer scale'.
These are the settings I am using. I tried letterbox integer fullscreen and still had the same problems.
<img src="http://seannoonan.co.uk/development/dev_noonanrun/settings.png" border="0" />
Please bear in mind, this is only happening when the project is scaling in any way - if I leave Fullscreen in browser to 'Off' then there are no problems at all. Every browser has the same visual quality (the performance varies however).
It seems only Chrome is able to scale correctly :(