Tim Peters added the comment:

Hmm.  I don't quite know what you're doing:  you said you're getting away from 
--with-pydebug, but these "bad leading pad byte" messages can't be generated 
unless Python is compiled with (at least) PYMALLOC_DEBUG defined.

That said, my advice remains the same:  whittle down the program (instead of 
fiddling with tools) to get a failing case as small & fast as possible.  In 
your "few dozens of seconds at most", many _millions_ of things happen, and 
there's scant chance of out-thinking them.

In the newest traceback (core.emerge.8425.gdb.txt), Python detected the 
corruption while running its cyclic-garbage collector.  Forcing gc to run more 
often may catch the corruption sooner (use Python's gc.set_threshold() to force 
more frequent collections).

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Python tracker <rep...@bugs.python.org>
<http://bugs.python.org/issue18843>
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