I don't know if this was what happened in your case, but I also recently built AFNI from source and noticed that 3dSkullStrip was missing. It was my fault: The problem was a missing option in my build script (which very slightly deviates from the normal AFNI build).
Specifically, there is a new dependency on libexpat, which was causing the SUMA build to fail. It's in the Makefiles I looked at (variables to do with GIFTI), but perhaps it's missing from the one you used, e.g. if your IT person built from source to work on an old version of Solaris.
