WebWarper cannot automatically correct some non-trivial operations with cookies. In particular, some problems are possible when using several subdomains (like www.yourserver.com and search.yourserver.com). Maybe, it will be necessary to review logics of cookies work, considering, that the addresses of your pages may contain "webwarper.net/ww/..." prefix .
Besides that, in client JavaScript, if the page is viewed via WebWarper ("if (window.___ww) {..."), then setting a "cookie" is possible only by "___ww_assignCookie(...)" call, instead of usual "document.cookie=...". In this case it is also necessary to keep in mind, that the address of the page starts with "webwarper.net/ww/..." prefix.