Sorry but the stream-of-consciousness style explanation you posted above is incomprehensible to me. Can you break down the issue you're having into very simple bullet points or something? I can't make sense of what you're asking. I loaded your file and the burger/patty fall down as expected. I don't know what the issue is supposed to be.
As for threading issues, are you using the latest build? Threading improvements were made recently. Either way, the sims you're running are bottlenecked by PhysX and PhysX threading works a little differently than regular tyFlow threading. Improvements were recently made in general tyFlow threading (specifically the ability to pin threads in the CPU rollout) which help prevent issues on certain AMD hardware (yours might be included there)...but I don't have the same control over PhysX threads currently, which could explain the slowdown you're experiencing.
As for threading issues, are you using the latest build? Threading improvements were made recently. Either way, the sims you're running are bottlenecked by PhysX and PhysX threading works a little differently than regular tyFlow threading. Improvements were recently made in general tyFlow threading (specifically the ability to pin threads in the CPU rollout) which help prevent issues on certain AMD hardware (yours might be included there)...but I don't have the same control over PhysX threads currently, which could explain the slowdown you're experiencing.