Gordon, make sure light thru trans is checked at the top AND in the GI section if you use any GI options. That definitely looks like an alpha issue. Many people who get the 5.03 update and above forget the second light thru trans option. The other possibility, which would be odd is that your alpha map is included in the texture and the alpha percentages in the channel are not set right.

No need to think outside the box....
    Just make it invisible.