I've had some major issues with views php when working with Search API. Specifically, anything I do in the 'value' code box just flat doesn't make it to the output field.
Today I located a patch that was committed into Search API Views (https://drupal.org/node/2096275) that seems to clear this up. Not sure if other folks are having similar problems, but wanted to put something on this side of the fence to tie them together. The linked issue is a Search API patch, but it is directly in relation to functionality in Views PHP.