It could be that when the sump empties the pump is sucking air slowing down the pump rate which is allowing air bubbles to accumulate in the U-tubes.
That being said you keep mentioning U-tubes in plural so I am assuming you have a dual U-tube overflow. The smallest dual U-tube overflow I can find is rated for 900gph. I did some guessing since you didn't provide any details on your plumbing or exactly what size your overflow is but anyway I assumed you have 4ft of head and used 3/4" hose or pipe for the return on your pump and when I calculated the head loss your pump is only returning about 600gph to your tank. If you follow my recommendation for pump rates your pump is just at the minimum recommended size to maintain the siphon in your U-tubes and this is only if you don't have any valves or other restrictions in your plumbing and your pump is operating at peak performance.
Another reason you might be having issues now is your pump is not pumping as efficiently as it did before you left and since its riding on the bottom of the recommended pump size your U-tubes are collecting air bubbles and losing siphon.
A quick fix is to just remove one of the U-tubes then keep an eye on it and make sure that the single U-tube can keep up.
Take my advice and don't add an aqualifter to your setup, I have used them and they are extremely high maintenance to keep them running somewhat reliably. Your U-tubes by nature are extremely reliable if you have the proper flow rate, but if you add the aqualifter they will be just as unreliable as the aqualifter is.