Teaching AFNI here at Wash U (St Louis), we've seen a few people with a peculiar problem: they can't type into AFNI popup windows, such as "Jumpto xyz".
The solution to this difficulty is to set an environment variable:
setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace
which applies when you are using a new version of the XQuartz server program. I've not seen this symptom before.
The best place to set this variable is in your ~/.cshrc file, so that it gets set for every invocation of the shell. If you are using bash
then you will have to use a slightly different syntax to set the environment variable.