I'm pretty sure weapon proficiencies are covered in 'racial bonus feats.'  Every type has the following entry in the description of the type, though they aren't spelled out in the individual monster descriptions as such.<br/><br/><div class="quoteheader"><div class="topslice_quote">Quote from: SRD</div></div><blockquote class="bbc_standard_quote">Proficient  with ... and any weapons mentioned in its entry.</blockquote><div class="quotefooter"><div class="botslice_quote"></div></div>The ... differs from type to type, but all monsters are assumed proficient with the weapons (including natural weapons) mentioned in their entry.  Since weapon proficiency is a feat, and alter self gives you racial bonus feats per the spell description...<br/><br/><div class="quoteheader"><div class="topslice_quote">Quote from: SRD</div></div><blockquote class="bbc_standard_quote">You acquire the physical qualities of the new form while retaining your own mind. Physical qualities include natural size, mundane movement capabilities (such as burrowing, climbing, walking, swimming, and flight with wings, to a maximum speed of 120 feet for flying or 60 feet for nonflying movement), natural armor bonus, natural weapons (such as claws, bite, and so on), racial skill bonuses, <strong>racial bonus feats</strong>, and any gross physical qualities (presence or absence of wings, number of extremities, and so forth). </blockquote><div class="quotefooter"><div class="botslice_quote"></div></div><br/>...I believe it is reasonable to infer that natural weapon prof is granted by the spell, though it could be rules-lawyered either way.<br/><br/>Not that it greatly matters, really.