Bass leaves after amp warms up?

Or should I say Atmosphere's.

Have you tried the speakers without the plugs? If so and it is even worse than I'd say we are on the right track. When you add the plugs you are lowering the "Q" of the speaker. Some speaker companies included different lengths of plugs so that the owner could tailor the speaker for the "Q" that works best for his room/amp combination.

The only other possibility is using a whisper fan on the amp so that it never warms up.

No matter what I try the bass changes character about 20 minutes or so into listening.
This happens all day long so I really don't know what to.
The enjoyment of listening is comprimised because I'm waiting for the bass to go out.
Plugs have not solidifed the bass response after many attempts.

Seems to work better,longer with no digital source plugged in.

You may be dealing with the inherent shortcomings of the gear. Nothing is perfect. Hot running amps such as tubes or ss class A may satisfy you more. Or be brave and learn how to set your amp up yourself. I would second guess anyone's adjustments, factory or not. Even (respectfully), Ralph's. I can pretty well guarantee it will change just in transit, never mind during break in. And I wouldn't trust factory break in periods either, (respectfully). I have never received gear back from a tech or engineer or brand new for that matter that didn't need tweaking in regards to offset or bias, even in reference to factory spec. And the sonic differences can be dramatic.