Upper hose is collapsing!

Okay here's the test...

Warm up engine and shut off, wait for hoses to collapse. Now, pull the overflow line from the bottom of your overflow bottle. The fluid should run out of the bottle. I bet the hoses expand and nothing leaks out of the bottle.

You said the overflow tube is sucking flat as well? If so the cap is working correctly and sending negative pressure into the overflow tube which is somehow plugged. If the bottle vent was plugged, it's sides would be sucking in also.