r430: fix a bug producing incorrect alignment

Ksw uses two rounds of SSE2-SW to find the boundaries of an alignment. If the
second round gives a different score from the first round, it will fail. The
fix checks if this happens, though I have not dig into an example to understand
why this may happen in the first place.
r431: added the MD tag to bwa-mem
Released bwa-0.7.6-r432
Release bwa-0.7.6a-r433