I am using build 2.5.0.86. After giving alpha maps in Scene Builder I publish files for STS. After publishing files from STS alpha maps are lost. What could be the problem? any workaround?

Should work just fine. What procedures did you use in STS that erased alpha maps? Try first to just open the file in STS, scale down the number of polygons just a bit, save and see if the alpha channel is still there.