I found a similar post to this, but not exactly what I am experiencing.
I am using Atahualpa 3.3.3
Issue disappears on 3.2.
Issue with IE 6.0.2900.2180 SP2. IE7, 8 and firefox3 no issue.

Post Header, byline, body, footer all the text disappears, only on certain posts, when the mouse cursor moves to the either the left or right sidebar links. Partially reappears when hovering over Post Header, byline, body, footer, but disappears again when cursor moves away from post.

Text is still present when clicking and dragging through the post.

This happens of how the post is viewed.

My guess, Sounds like a hover issue with IE6 CSS.

Please help.

1) have you made any changes to the Atahualpa code
2) have you entered any HTML or CSS Inserts
3) if you disable all your plugins does it still happen
4) is there something common about the posts that thei happens in - ie. they all have a image in them or they have a youtube video
5) what's the url

1) have you made any changes to the Atahualpa code
No

2) have you entered any HTML or CSS Inserts
I did, but reset theme and still having same issue

3) if you disable all your plugins does it still happen
yes

4) is there something common about the posts that thei happens in - ie. they all have a image in them or they have a youtube video
No, but One post on the home page with the first image tends to through the disappearing
5) what's the url
the site is on an intranet

ok, just did a google search and this is known as the IE6 Peekaboo Bug (oh, I like that name!)

One solution you could try is to add this to the CSS Inserts

h1, h2, h3, h4, h5, h6, p {
position: relative;
} 

I don't if it will cause other issues and I can't test it myself since I don't have a copy of IE6

Sorry, guess I could of googled it. I figured the forum would be easier (already one of those weeks). Thank you fast response.
Great theme. Thanks for everything.