You already have a bunch of discussion on how "k" can seem dismissive as it's the lowest effort affirmative reply possible, but I'd add that "K." can seem worse, because it's the same message with more effort - if everyone has understood/assumed that "k" is the lowest effort/energy communication, capitalizing and punctuating it indicates that you do have the extra energy, you just choose to spend that energy on emphasizing the dismissive response, rather than on using a different one. It has the same connotations, but more emphatically and more intentionally (or, that's how it comes across).
I also think in general taking the effort to use correct punctuation and grammar seems more formal, less natural, and hence more emotionally distant. It can also seem more emphatic or assertive, like by using more correct grammar/punctuation than everyone else, you're positioning yourself as generally more "correct" than they are. The combination of emotional distance and implicit high ground can come across as a bit hostile, or at least standoffish.
The reverse could also be true - if you were in a culture or context where everyone else was using correct grammar and punctuation and you weren't, it could come across as implying that they're not worth caring about. For example, in work communications, or maybe when talking to members of an older generation or people from a country that uses more formal language.
In general, probably the smoothest approach would be to observe how others in a given circle communicate, and try to match their level of formality. I guess this is basically masking. If you'd rather not change how you communicate to fit in, you could explicitly discuss this with people - essentially say, "hey, I'm aware that my natural style is different from yours, and I want to be clear that this isn't indicative of my emotional state, or attitude to you, or any intended tone, this is just my natural baseline".
At the end of the day the options will always be a) mask, b) be awkwardly explicit, or c) get used to being misunderstood.
... this was really meant to be a quick addition about the difference between "k" and "K." but sometimes my comments turn into essays for no good reason. Hope something in here was useful anyway.