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Closing as invalid -- this is a bug in the OP's script, not
in Python itself.

The error is obious when the code is simplified further by
in-lining the function.  Also, it helps to explicitly set
the initial values of variables between the two sections:

#!/usr/bin/env python
num_elem = 100

key_src = range(num_elem+1)
keynums1 = key_src[:]

assert key_src[-1] == 100
for _ in xrange(num_elem):
    keynums1[key_src.pop()]

keynums2 = [0]
for _ in xrange(102):
    key_src[keynums2.pop()]


I think your coding error was in assuming that keynum2 held
a different value before the second half was run.  If so,
that could have been found by using pdb or by inserting
print statements to reveal what is going on.