R. David Murray added the comment:

The install log shows the file being copied into place:

copying build/lib.linux-x86_64-3.4/_sqlite3.cpython-34m.so -> 
/soft/pyt341/lib/python3.4/lib-dynload

This does not line up with the fact that you said the file did not exist after 
the install.  Something would have to be deleting the file after it got copied 
into place.  After you run make install, is there anything at all in 
lib-dynload?

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<http://bugs.python.org/issue21950>
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