I cannot reproduce the trouble.
This is my result.
% cd /tmp/global <= GLOBAL source code
% mkdir /tmp/tags
% gtags /tmp/tags
% ls -l /tmp/tags
total 2024
-rw-r--r-- 1 shigio wheel 16384 Sep 2 00:12 GPATH
-rw-r--r-- 1 shigio wheel 1392640 Sep 2 00:12 GRTAGS
-rw-r--r-- 1 shigio wheel 434176 Sep 2 00:12 GSYMS
-rw-r--r-- 1 shigio wheel 204800 Sep 2 00:12 GTAGS
% htags -d /tmp/tags /tmp/tags
% ls -l /tmp/tags
total 2025
-rw-r--r-- 1 shigio wheel 16384 Sep 2 00:12 GPATH
-rw-r--r-- 1 shigio wheel 1392640 Sep 2 00:12 GRTAGS
-rw-r--r-- 1 shigio wheel 434176 Sep 2 00:12 GSYMS
-rw-r--r-- 1 shigio wheel 204800 Sep 2 00:12 GTAGS
drwxr-xr-x 9 shigio wheel 512 Sep 2 00:12 HTML
% _