Problem: ArcScene: base surface layer adopts transparency of draped vector layer
Given two layers in a scene, a feature layer and a TIN, if you drape the feature layer on the TIN, set the feature's transparency, save and reopen the document, the TIN layer will end up with the same transparency as the features.
This is a known problem.
Solution or Workaround
When setting the base surface for the features, specify the location of the TIN on disk rather than referencing the TIN layer in the scene.