I have the same warning. When I go to validate my files, it says that everything is fine with my files; it just won't align.
My error is different than yours because the first pass alignment doesn't return an error in verbose, but when it moves on to the second step of "generate alignment' it returns the warning that you have above.
At the end of the process, the INFO says "Exporting textgrids to (path)", "Finished exporting textgrids to (path)", and "Done!" When I go to that particular folder, nothing is there and it is completely empty.