The description is the same as in the linked bug report. I think it's a webkit problem, and not a Prototype one. Note that this doesn't happen always, you may have to reload multiple times to see the bug. It helps if you press reload and move Safari to the background. It's more frequent in Safari 3 than in the today's nightly build (r28586) but it still happens.
I consider this serious because a lot of sites are using Prototype, and will upgrade to the latest version.
>I have the following problem and don't know how to come by this. If I include prototype.js and
>scriptaculous.js Safari gets a problem with coloring the background of the viewport. It only works
>where you placed some div, the rest of the page won't be correctly colored at first. If you resize the
>window everything is fine.
>I did test this with Safari 2.x/3.x on OS X 10.4.11, other browsers (FF 1.5+, Camino, Opera 9, IE 6+
>on Win) are fine with this page. Also confirmed by other Mac Users using various OS X versions and
>Safari versions. Here you can take a look at the issue <http://www.fightex.com/test> and here you
>can find a screenshot <http://www.fightex.com/test/scr_safari_scriptaculous_bg_issue.png>
>Scriptaculous Version: 1.8.0 Prototype Version. 1.6.0
Confirmed with Safari 3.0 (523.12) with original WebKit on Mac OS X 10.4.11 (8S165).
Also confirmed with WebKit nightly r28586 on 10.4.11.
BTW, I realize this bug has a reduction, but it requires the full prototype.js and scriptalicious.js libraries to be included. There is probably a smaller reduction of the bug that's possible.
This is probably bug 34913.