Sounds like the hose on your manual vac might be leaking air into the system which is causing the pump to lose prime. Any air, even for a fraction of a second, that gets into the stream of water going to the pump can cause the pump to lose prime. You always want to avoid this, when possible, because the water cools the pump and it can overheat when sucking air or trying to regain prime. When you are connecting the Barracuda, you're probably letting air into the suction side from the cleaner and the hose. This interruption in water flow will be enough for the pump to lose prime. I always hook everything up to the hose, be it the manual or automatic vac, sink the vac and THEN hook the hose up to the skimmer. Sometimes I'll even sink the hose segments to get them full of water. Anyway, always try to avoid getting air into the system. I know you are getting air in because you say you see bubbles coming out the jets.

To check the hose for air leaks, pick each segment up out of the water while hooked to the skimmer and listen for a hissing sound. Most of the time, if a hose is going to suck air, it'll do it at the hose joints. If you hear the hissing noise, replace both segments. I've gotten a lot of cheapie hoses that don't mate up well.