I downloaded a content report (although it was a keyword and not custom), and it was indeed empty (using the ContentOnly flag). I know I have content clicks, because we have our own tracker.

Hmmm...so you're suggesting multiple reports, and merging the data? On the adwords site, I can create a custom report, which includes all of my data. I should somehow be able to mange this from the api. Merging multiple reports sounds more cubersome than it needs to be.