Your puzzlement about blowholes in PTH solder connections during reflow soldering comes from: * Boards are hydroscopic. So, moisture content of the board is uniform. * Gold plating is uniform. * Nickle plating is uniform. * Copper plating on your PTH is not the same as the copper plating on your SMT.
This difference comes from the board fabrication process. Fabricators: * Purchase unform thickness of laminate with copper attached or copper sheet. * Plate copper in through holes after drilling the holes to [hopefully] your specification.
Short term: * This in-process portion of the lot needs to be baked to remove moisture from the board and resoldered. Search the fine SMTnet Archives for bake recipes. * Assuming the lot can't be rejected, future builds of this lot of boards need to be baked to remove moisture prior to soldering.
Longer term: * Require that board fabricators plate greater than 1 thou of copper in through holes. * Institute a procram to check boards at incoming, so that issues like this are caught earlier in the process. * Develop better methods to limit the amount of moisture absorbed by boards. This may involve controlling the the environment of the board storage area, storing boards for shorter periods of time, packing boards in protective material prior to storage, and controlling the environment of the boards assembly area.