The threshold is periodically increased to allow for karma inflation, but usually that gets announced, and I've not seen anything recently. As far as I'm aware the threshold is still at 500 - nothing has turned up in my search of HN to suggest otherwise, but search is poor at finding this sort of detail.
Are you confusing this with topic downvotes? They don't exist. Do you know where to look for the comment downvote link? It's a small gray arrow under the upvote arrow just to the left of the name of the commenter.
When I first crossed 500 I noticed I could downvote replies but not top-level comments. Not sure when it happened, but now I can downvote top-levels too.
I wish I could turn off the downvote arrow. I never use it, and I have to be careful not to click it by mistake when upvoting.
You can't downvote comments over 48 hours old - perhaps that's the effect you're seeing.
I usually find that even here on HN, the symptoms people report are not actually what's happening, but are filtered through their incorrect assumptions. It is important to report what you see, not what you think is happening underneath. It's so easy to fall into the trap of reporting what you think must be happening.
Are you confusing this with topic downvotes? They don't exist. Do you know where to look for the comment downvote link? It's a small gray arrow under the upvote arrow just to the left of the name of the commenter.
If none of this applies then I can't help you.