You can tell if it's the same problem I had by checking whether not only 3dSkullStrip but everything SUMA (including the suma command) is missing. There are also some error messages at the end of the SUMA build, although those scroll off the screen very quickly and don't cause the overall AFNI build to fail. Like I said, I've got a non-standard build procedure so in my case I just needed to update some options to ensure that libexpat was linked properly. In the standard Makefiles, the variables to look for are USE_GIFTI and LGIFTI, as well as SUMA_LINK_LIB.

But even with a standard build I think one likely scenario is that you're using a Makefile for your platform that references libexpat even though you don't have it installed on your system. Check to see that it is in fact installed, or you can try deactivating it in the AFNI Makefile by commenting out the USE_GIFTI variable (I haven't tried that though).