I have seen several other posts with people who had the same issue, can I please get some help?
Here is a link with an issue nearly identical to mine: http://wordpress.org/support/topic/jetpack-stats-lost-after-deactivatingreactivating-1?replies=3#post-5128517
I am having the same problem but the most important thing is that I lost my subscribers. Could you take a look at my post Jeremy?
I figured it out. I am using a droplet on digital ocean. I enabled mod_rewrite in apache but I did not change the AllowOveride value in my virtual host definition file to all. For anyone else who might have this problem:
<Directory /var/www/>
Options Indexes FollowSymLinks MultiViews
AllowOverride All
Order allow,deny
allow from all
</Directory>