It appears you're still experimenting with this, but bear in mind that the standard overlay-style cart that appears "inside" your page is treated as a separate cart from the "fallback" cart that appears in a separate window/tab whenever the overlay cart can't work for some reason -- i.e., items added to an overlay cart won't appear in the fallback cart, and vice-versa.
If you want to use the overlay-style cart, pasting the button code directly into the raw HTML source code, separately from iWeb, is the method you should use. This discussion covers some more tips you may find useful for using iWeb with E-junkie:
http://www.e-junkie.com/bb/topic/3164