You didn't mention which type of Web Server you use for the CGI-Extension portion, as it is called during WebAccess setup. Using Microsoft IIS here for our webServer. Our WebAccess would mess up & traced it to some publishing being done on the WebServer with Microsoft Front Page. Front Page Extensions would mess up the WebAccess part. Could connect, but it would not find the Groupwise Server, or it may find it, but would end up with a bunch of garbage characters. (MS-Java problem, so I have heard?)
To repair it, we had to completely remove all WebAccess related directory structure on the Web Server side. There are two of the CGI directories-\Cgi-Bin & \GW5. In addition, we had to remove the WebAccess gateway Directory structure on the Groupwise Server. This is normally located in the GW gateways dir-\GrpWiseSystemDir\GWDomainDir\WPGate\TheWebAccessDirectory. Also remove the WebAccess Gateway Object from the NDS tree.(You may want to record property values BEFORE deletion)Be sure all NetWare & GW is patched up to the most recent versions. After patching, be sure your tree is stable and replicated. Then install webaccess only from the Groupwise Installs directory, which is set up when you install or patch Groupwise. If it don't exist, manually copy the GW Internet files from the CD, and then run the GW patch on it. Be sure you Map a drive to the Cgi-bin directory of the Web Server BEFORE creating the WebAccess object in the NDS tree. Once you click "OK" to the Gateway object,it will create an important file called "commgr.cfg" in the \Cgi-Bin of the Web Server.(Tip-You may first try to simply rename this file, and click OK to simply create a new one before you do all of this work-Sometimes it works) After that, create &set up your WebAccess gateway using F:\public\win32\Nwadmin32.exe. I used the normal NwAdmin and spent two days to figure out that Nwadmin was the wrong version for creating new GW