with an engine mounted impeller, if the water line drained of water when the boat was pulled out, unless your muffs fit really well you can have this problem. Not as common on an Alpha since the raw water impeller is right in the lower gear housing and the water doesn't have to travel far before the impeller can pull it in. On a Volvo, or Bravo system the water has to travel up 1.5' and approx 3-4' forward to reach the impeller. I used to use the Tempo style muffs dual inlet and the last pair of them I used (right after my top end overhaul) it seemed that the rubber was stiffer and I could not get my Cobra to prime easily as I had in the past. The Cobra is a little different from the Alpha in that the impeller is in the upper gear housing (very easy to replace) but water has to travel about 1.5' up to reach it. I switched to the Merc/Quicksilver round ones with the metal rod clamp and it was 100% better. The Merc muffs are softer rubber that conforms to the shape of the lower unit better and the clamp holds it tight. Well worth the extra $$
After starting the engine you should see water getting exhausted under the transom mount within seconds. If not then its not pulling in water and remember impellers can't move air only water.
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notice how much water is exiting the transom mount in the vid.
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