You simply don't have the required 50 reputation points to comment on Super User.
You can however still comment on your own questions or answers.
A question that you offered a bounty on is still not considered your post.
You placed a bounty on that post but it still doesn't belong to you; the comment limitation is still enforced.
There is something slightly odd with loosing privileges from offering a bounty, but essentially it is not because of the bounty; it is because of the reputation drop. A 10.0K user offering a 50 rep bounty won't have access to the mod tools, but the reputation decrease has nothing to do with his ability to contribute to the community.
There's a hole in the logic there, and I'm pretty sure it's there to not unnecessarily complicate things. I'm drifting dangerously towards a feature-request in an answer to a support question so I'll leave it at that!
Privileges = Reputation + Offered_Bounties