Getting blacklisted for showing appreciation in the comments section?

Is it viewed negatively to express appreciation in the comments section of a giveaway?

No, just pointless at best.
Like, would you thank the seller every time you buy a lottery ticket?
Well, that's up to you, I guess.

But in smaller crowds, like group/whitelist/forum giveaways, It's actually more likely to be be appreciated, especially when rare and/or expensive games are being given away.

I've tried to express my gratitude for every single giveaway I've entered, because I think that's the least I can do, but I'm getting the feeling I wouldn't have gotten half of my blacklists if it wasn't for leaving those comments.

Yeah, that's definitely it.

Or rather, the simple act of leaving a thank you comment in a giveaway, in and of itself, doesn't really mean much, and that's not what you are being blacklisted for.
But when a user spams the exact same copypasted comment in every single giveaway they enter, that's usually a dead giveaway (pun intended) that the account might be using some form of automation (like the infamous autojoin scripts).

THAT is what you're being blacklisted for, at least by those unwilling to do the legwork to figure out whether you're actually a bot; they'll just assume you're one, blacklist, and move on.