Could be we just don't understand your terminology. What do you mean with "cleaned the entire thing out"? Did you replace all the sand? Or did you backwash? If you backwashed, did you complete the process with a 30 second rinse cycle? The rinse cycle packs the sand back down and prevents it from blowing back through the return.

Is your multiport valve set to filter? Or do you have it on recirculate while vacuuming?

Does the gasket on the multiport valve need replacing?

Is the handle of the multiport firmly seated in the appropriate slot?

Filtering dead algae can take quite a few days. Have you ever tried skimmer socks? I like them for catching small debris before it gets in the filter.