We use the air/compressor method for winterizing, always have. Never had the issue described here.
However, here is I think where the difference may be: Even though we blow out all lines with air compressor to winterize, before doing that, I pump just a little bit of antifreeze through the water pump, just enough to fill the pump itself and its input line with antifreeze to protect it from freezing. Once that is done, I hook up compressor and blow out the lines.
I am hesitant to push compressed air through water pump (from input side), so letting it pump a little antifreeze through is only way I know of to get water out of the pump itself and protect it from freezing. Soo, even though we use compressor blow-out method, my procedure has still always been to use just a little antifreeze in the pump, to protect it (as well as in all the drain traps, obviously).
Anyway, might want to try this approach next time, see if that doesn't help. Perhaps the pump having some antifreeze in it will 'prime' it a little better, and allow it to start pulling water through easier when you get it back out in the Spring.