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I'm taking a guess that when it looks for page map stuff to delete, it first looks for the Google Play pagemap file (Ops/_page_map_.xml) and the Manifest items (_page_map_.xml (_page_map_)) and either pulls the GBS anchors out based on those or looks for the self-closing tags itself. But, once it removes the pagemap file and manifest items, later runs (when the non-self-closing anchors have been self-closinized) will say "no such pagemap/manifest objects exist, therefore no GBS anchors exist. And it quits. Total WAG on my part. But, it seems to explain the behavior.
So, as you say, the work-around is to not use the "remove page map" options until after doing a run and getting those tags self-closed.
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