I've noticed that Site Builder has been funky lately too. I was updating one of my websites and noticed several glitches.
1) Tried adding some Java Script to my site (such as the Kontera code as well as ad code from Link Referral), but the java script code did not seem to load
2) The spacing on site builder editor is decieving (especially when you load the published page on your browser)
3) When I tried adding the guestbook plug in to one of my pages below a text box I had, it got mixed in with the text on the published page.
Another suggestion:
There ought to be an easier way to add Google, Bing and Yahoo verification code to your site (for the sake of search engine optimization).