Your post does not contain enough information to allow us to help you.

...these scripts have been running very well from the command line....

...the batch file does not run as it does in the command line...

Archetypically, differences between the runtime behaviour of scripts running from the command line and the same scripts being run from a webserver are due to the fact that the userid used by the webserver does not have the same rights accorded it as the real user running it from the command line. VSS with try to authenticate the user running it, and unless you have given the userid that your websever runs as the appropriate authorisations to act as a proxy for everyone that will use the web-based version of the script, VSS will reject the attempts to obtain information, much less commit changes.

...it does not take the values I pass from the html...

You don't show us how you are invoking the batch file from your CGi script, so our attempting to work out why the parameters are not making their way into the batch file correctly is impossible.

As others have pointed out, it would be entirely possible to set the environment variables required by CSS directly within your perl script prior to invoking VSS as a child process and avoid one level of indirection, but unless it is possible (and safe!) to grant the webserver runtime account the appropriate authority to act as a proxy for the users invoking the CGI, you aren't going to achieve your goal.