If you are using Cpanel, I recommend that you go to your database and click ‘repair’ to fix any possible problems there. Check to see if you’re comments are still in your DB or not. Check to see if there are updates for plugins that you are using, out-dated plugins may cause your comments to not appear. Check your wordpress directory for error_log file to see any errors recently.
Also, did you disable all your plugins before upgrading?
This isn’t a big upgrade so you must have done something wrong.
The following files were the only ones to change, and there were no DB upgrades, so you didn’t really have to run upgrade.php
Check here for the following Upgrade Changes from 2.6.1 to 2.6.2:
https://trac.www.ads-software.com/changeset?old_path=tags%2F2.6.1&old=8849&new_path=tags%2F2.6.2&new=8849
