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After taking a look at the source code my guess is because the pointcloud_to_pcd has a queue of 1. This means that if it is processing some message n, it is perhaps that by the time the callback is finished running n+1 is no longer the most recent message and thus is ignored.

  sub_ = nh_.subscribe (cloud_topic_, 1,  &PointCloudToPCD::cloud_cb, this);

Whereas bag_to_pcd will just iteratively inspect the messages in the bag.