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How high is the water in the pool? The extra suction through the skimmer by having the MD plugged may be causing a vortex.
Alternately, the extra suction may be enough to draw air through a questionable seal or connection on the suction side (even the valve itself). To check this, dribble water on any suspect area with the pump running and see if the bubbles in the pump housing lessen.
Sorry I can't go into greater detail now, but this is a very busy time of year for pool dudes. I'll follow this post if you need more info. Also, I know searching could dig up some of my previous pearls of wisdom on this issue and there are a bunch of great folks here that will also assist you.
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