Clint, I can now answer your questions, at least partially.

* If I renice the program, the effect is likely gone. However, I will be
sure only after a longer period of testing.

* Other programs run swiftly (also without renice-ing  prog.x).

I will comment on this issue sometime next week or so,  as soon as I
acquire more evidence. It may be useful to remind the following info
from my orginal report:

The long delays in  scp procedure occur if machine B was NOT exposed to
an scp or ssh demand for a longer period of time. (Typically I face the
problem in the morning.) If an scp transfer is finally accomplished then
I can start a new one which already works without a delay.

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https://bugs.launchpad.net/bugs/782092

Title:
  ssh server extremly unresponsive

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