Strange Audio problem.

I upgraded the audio in my Taco because the stock sound was no-bueno. Stock non-JBL HU with: JL 650 components front, Kenwood coax rear, Arc Audio amp and JL sub. Installed by an audio specialty shop that I trust. Sounds great now but has an odd glitch as follows:

When I've driven for a while (i.e. 1 hr commute), and lets say I stop at the store before I get home. When I return and restart the truck, the audio is muffled (almost sounds like its under water). After it's sat for a while it works fine. Strikes me as a possible heat issue, but I know next to zip in this area.

I can recreate the issue, and the installer is going to diagnose and fix no-charge when I can get it in and leave it for the day (hate to be without it for a whole day though LOL).

Thought I'd check here to see if any experts might have an idea what could cause this?