strange i am having no problems using webroot and renewal via webroot.ini see Let's Encypt Enters Public Beta
contents of my /etc/letsencrypt/webroot.ini
# webroot.ini general config ini
rsa-key-size = 2048
# Always use the staging/testing server
#server = https://acme-staging.api.letsencrypt.org/directory
# for beta invitees
server = https://acme-v01.api.letsencrypt.org/directory
# Uncomment and update to register with the specified e-mail address
email = myemail
# Uncomment to use a text interface instead of ncurses
text = True
agree-tos = True
renew-by-default = True
authenticator = webroot
i define the webroot path on the command line
letsencrypt -c /etc/letsencrypt/webroot.ini --user-agent centminmod-centos6-webroot --webroot-path /home/nginx/domains/le12.http2ssl.xyz/public -d le12.http2ssl.xyz certonly