I admittedly do not use B|T in a VM,ever; so this could be more complicated than first look. What really jumps off the page at me though,is you that are having a user permissions error while logged in as root (but within a vm); and using the chmod flags u+x. the u flag sets permission only to the specific user, and the entire thing appears to be a permissions issue. have you tried using simply chmod +x yet? by ommitting the a,u,g,o flags.; using simply the +x flag will apply execute permission to all users.
hopefully this helps you. it's the first thing i would rule out if having this sort of problem,anyway.