I wish there was a way to see the math, like we could with the old character sheet, for at least the defenses. It took me a few minutes to figure out why my Knight's AC jumped up a point, until I realized it had automatically given the bonus for masterwork plate to AC. I couldn't find masterwork armors listed separately at all.
One neat benefit of the builder, is it has a little information that the compendium does not yet have. One of my player's just acquired the Anarusi Codex tome implement, and when I looked it up in the builder I found that it had been given the Rare type. So check your items for new rarities! Maybe there's more Common or Rare items that haven't been noticed yet. No Staff of the Magi yet, Anarusi Codex is the only rare implement thus far, not counting weapliments. Holy Avenger is still Uncommon, so I guessing that some things will change when the DM's kit information is added.
I haven't had any technical issues with the program yet, but I haven't tried Importing a character. Running fine and faster than the offline builder did in some ways in Safari 5.0.2 on my Macbook with the latest Silverlight update.