In all of the option for the user Control panel in the Appearance tab have:

themes.php?page=atahualpa-options#

as their link.
I was wondering how do I get these working?
Did I miss something?

what version of Atahualpa and WP?
what is your url?
if you swap to twenty-eleven - does it's back end work?
How did you install Atahualpa?
Who is your host?
did you check the error log on your host to see if there were any eror messages?

Originally Posted by juggledad

what version of Atahualpa and WP?
Atahualpa 3.7.7-WordPress 3.4.1
what is your url?
http://k3jc.org/jayceeslately
if you swap to twenty-eleven - does it's back end work?
Yes
How did you install Atahualpa?
Through Wordpress (and activated)
Who is your host?
GoDaddy
did you check the error log on your host to see if there were any error messages?

Yes (and no)

check to see what version of php you are running - it should be 5.x
do a google search with 'godaddy php'

All my sites are running on PHP 5.3
And it works fine on my other Atahualpa Install:
http://www.jesterz-court.com/wordpress

what is different about this site?
do they all run on the same host or is this different?
are they all at the same WP level?
Atahualpa version?

it has to be something about the environment that is different, of course figuring out that difference is the challenge

do a phpinfo on both sites and look at the differences

they are on the same hosting
Same WP and Atahualpa.
Installed both within minutes of each other

It could be that the install timed out. I'd suggest manually reinstalling the theme and see what happens