Is there a parameter to make FMPP fail when it is unable to find a value for a variable in the template? right now it just leaves the text intact with ${} if it cannot resolve a variable.
Something strange is going on there, because it does fail and by default even aborts the whole batch processing if you refer to an undefined variable. Also, it doesn't leave ${}-s in the output, because all the ${ and } are "parsed away" before the template could do anything. So I suspect the value of those variables is indeed the string "${}", or you have some tricky #escape in the border/footer/header settings, or something tricky like that. (If you can provide a minimalistic example to reproduce this, I can certainly spot the reason.)