I think someone else is having this same sort of issue, but I did not want to hijack their thread so I am posting a new one. I had this issue before and solved it, but I just can't remember what exactly I did to fix it. For some reason the texture on certain objects look transparent when the canopy is closed, but if you open it the texture is normal. I have tried to remove the rvmat. for the canopy, but issue still persists.
By meatball0311 at 2012-04-24
For some reason I did this (Reply #2) before and it did not solve my issue. But I did it again and now it works. My bad....
Select the canopy glass and then goto 'Faces' tab and select 'Move Top'