The problem seems to be related to the way PennController handles cross-trial references to Var elements. In this case, a newVar command with .settings.global() inside a Header was causing an “undefined” error the first time the trials were run only—the second time, the Var element having already been created the first time seemed to “fix” the error, in a way.
This bug, and other bugs related to Var elements, should be fixed in the next (and upcoming) release of PennController, version 1.7.
Jeremy