So I have some more info on this:

My application had a hierarchical block, inside which I had a block (called
"chopper") that was setting the set_output_multiple.
This block was the source of the warning:

gr::log :WARN: flat_flowgraph - Block (chopper0) max output buffer set to
6656 instead of requested 8192

I don't know why this warning was given (I suspect the size of the output
buffer is forced to be a multiple of the set_output_multiple and less than
8192?),
but when I reprogrammed the "chopper" block and removed the
set_output_multiple from it,
neither do I get the warning nor does the application crash (when i run it
with controlport on).

So i have solved the problem but i have not understood why it crashed in
the first place.
This may indicate some hidden bug in the code...

So the questions are the following:

1) why is it that the flat_flowgraph gives this warning when trying to
flatten a hierarchical block which contains a block with a
set_output_multiple ?

2) why is it that with this choice of output buffer the application crashes
when controlport is activated?

best,
Achilleas
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