Ryan,
Could be a conflict between our box.js cart script and some other JS your page is loading. Whenever the overlay-style cart can't be displayed for any reason, the buttons work in "fallback" mode by opening a popup window/tab to display the cart, so that seems to be what's happening for you. Sometimes conflicts can be resolved by simply rearranging the order that scripts load into your page; otherwise, you can remove the other scripts one by one until you find which one resolves the problem when removed. Note that the SCRIPT portion of your View Cart code can be moved anywhere you wish in the page, even up into the page HEAD; just take care to keep that block of code together in its original order -- i.e., with the box.js line after the function EJEJC_lc(th) { return false; } part.
Bucko,
Have you tried saving directly from HTML view after you paste the code, without switching back to the visual editor first? The tips on this help page may help you get the code pasted in exactly where you want it:
http://www.e-junkie.com/ej/help.site-blog.htm