When I give a user the "Administer Comments" permission, and they don't have the "Administer Nodes" permission, comments are disabled on any node they create.
The site default for comments is read/write, but for users with that specific permission comments get disabled.
They also can't see the comment status box when they try to create a new node, so they can't change the status from disabled to read/write.
Here's another bug that talks about something similar, although, I didn't completely understand everything they were talking about:
This bug is critical. It means that I can't give a user the Administer Comments permission at all, because it disables comments on any node they create.
Comments
Comment #1
gregglesMarked http://drupal.org/node/40569 as a dup of this issue.
And actually, this issue is a duplicate of http://drupal.org/node/29337