Due to a WordPress requirement for themes, themes can no longer use the EVAL() function. This
means that since 3.6.5 custom PHP code isn't possible anymore in the Atahualpa Theme Options.
Atahualpa was one of few themes, if not the only theme, to allow custom PHP code to be inserted through theme options. The philosophy as to what themes should or should not be able to do (i.e. which PHP functions they can use) has been tightened up quite a bit lately by WordPress, so in order to stay listed on wordpress.org we had to remove this 'custom PHP' feature.
Check wordpress.bytesforall.com and forum.bytesforall.com for possible workarounds or even alternative theme versions, if you cannot live without custom PHP.