Rewriting session handling would be rather hard way to approach the problem.
I was working with epesi on ModRewrite and had zero problems with the session.
To recap your configuration, check if I get it right..
I'll be writing as if your domain name was "domain.com" and epesi was under "epesi.domain.com"
So, in epesi index.php file, modules, etc. is to be found in /var/www/users/domain.com/subdomains/epesi/
There's .htaccess file in /var/www/users/.htaccess
When given address epesi.telaxus.com, apache first targets /var/www/users/domain.com, ModRewrite kicks in and it's pointing to the right folder.
I recreated exact same conditions on my epesi and it's working.
The only thing we have different then is EPESI_DIR variable. If I remove that, I receive an error that EPESI_DIR couldn't be determined and to set it manually in config.php.
I'd check this lead. You said you deleted EPESI_DIR from config.php. Try to bring it back and set it to "/".
Please tell us if this works for you.
Kind regards,
Arek