For me, in Chrome on my high powered desktop, the slow version runs smoothly, but not as fast as the compiled sample program as an EXE (which sets LimitFrameRate at 80 fps). LimitFrameRate is used in the HTML5 code to determine the parameter for setInterval, the function that tells JavaScript to call a function periodically every X milliseconds. So if the CPU hadn't hit its limit, the game should run at the same speed in a browser as it does in a compiled EXE. When I run the other simplified version, it runs fast even in a browser.
I tried on my laptop where I have FireFox installed too. There, both the old and new versions run slower than the compiled EXE, and the slower one is noticably slower. On my desktop in IE, the performance is similar between the 2 versions. I think it still runs slower than the compiled EXE (although very smooth), and the old version runs slightly slower than the simplified version. I have not verified this -- just visual reaction.