I have WP version 2.8.4 and I use customized Atahualpa with Viper's Video Quicktags.
This is my first Atahualpa site so bear with me.
Most of things I have worked out, but there are a couple of things that are not working for me.

The most annoying thing is that short codes (and the link inside them) used by Viper's plugin show up in the excerpt as a text.
It would be a nice idea to get rid of these links or make wp process them so the embedded video shows up.

I have searched around and it seems the only working solution is to add this

add_filter( 'the_excerpt', 'do_shortcode', 11 );

line in the functions.php file excerpts section. Maybe it has worked for someone (with a different theme?), but in my case it just makes everything inside the short code into a link.

Viper's developer pointed out that if this isn't working for someone then they are out of luck. I believe that there has to be a solution and I don't believe I'm the only one with this problem. I tried to place this code in different section of the functions.php and tried different versions of the code, but with no result.

Maybe someone here could help me?

What version of Atahualpa and PHP?

what have you got at ATO->Configure EXCERPTS->Don't strip these tags?

What is the url pointing at an example?

Atahualpa is 3.4.1
PHP is 5.2.6

In the don't strip these tags section i have <p>

my page is dq.lv (i have now selected to display full post everywhere, but would like to switch to excerpts in archive view if this problem is solved).

also I to have some problems with featured content gallery, but i think i will fix that today.

can you switch to excerpts so I can see the issue?
Also try adding <a> to the 'In the don't strip these tags' - by default, all the html in a excerpt will be stripped, so if you have a <div> or <a..> or <ul> - you need to add them to the list of the do not strip

Ok. I switched on the excerpts in archives (here is a link to an archive page with some short code - http://www.dq.lv/?m=200909&paged=3)

Added also <a> to the don't strip section.

What is the actual contents of the post? do a cut and then hit the little HTML button above and paste the code between the [ html ] and [ /html ]