Didn't it say not to upload the styles?
Standard upgrade procedures are to not upload the includes/ styles/ or cache_builders/custom folders.
If you choose to upload files in the styles folder you'll want to take special care that you do not upload the wrappers.php file.
As for the column width issue, the shoutbox's input box is now 30px wide; in earlier releases it was 15 or 20px wide; the issue is that the columns' width varies user to user based on how gigantic their screen resolution is, so users with a smaller screen will have the shoutbox column forced larger to accommodate the size it wants to use when drawing out on the screen.
Edit templates/default/island_shoutbox.tpl and look for the input line and adjust the size variable.
