[archaeolept]

it sounds like someone may have modified the tga instead of the .map in order to rectify the obvious original connectivity problems, as what you report sounds pretty similar to the original issue.

it is easy to edit .maps to correct connectivity, luckily.

also you may want to double check that none of the magic sites have been taken out of the game. I know many were added in DomIII; possibly some were taken out.