Why are my doughnuts raw in the middle?
The answer is simple: your test batches were less airy, and more dense.  The heat from the oil was likely unable to penetrate the dough as effectively and cook the interior.

If the recipe turned out properly the first time around, that's probably not the issue.  If your concern is with storing the doughnuts  (though how you would have any left is a mystery to me!) then you may want to check out more effective methods of storage.  There may be some helpful guidelines in this thread.