Trying to figure out how this can be accomplished... =/
The regular Google Analytics code doesn't track in a javascript lightbox popup, so we had to use a Analytics custom event for tracking.
I believe we might be running into the same problem now with our Google Adwords conversion pixel that we're trying to add into another lightbox popup after the ones with Event Tracking on them.
I can't find any other topics anywhere on this subject. Is this possible or able to be done using another method similar to how Event Tracking can be used with Analytics?