Cross-compiling Python is a huge PITA. It supposedly got better w/ 3.x, and some of that got backported to Python 2.7.x, but it's either broken, or I'm too stupid to understand how to use that properly, so I'm currently
hacking around it.
Cross-compiling Python binary modules is even more fun. (not).
As for the initial subject, check if there isn't a permanent LD_PRELOAD in place, I can't remember if the Kobos do this, but the Kindles have such a permanent (/etc/ld.so.preload) library injection in place, for the express purpose of enforcing some env vars.
(Such a thing can be easily caught through strace and/or the ld debug vars).