Worried about new kitten

Huh, that sounds... odd, but hard to tell. Is she still eating and drinking and using her litter? Does she like to play? Does she do the crawling thing at certain times? Is it rubbing some part of her on a carpet? How old does the vet think she is? Does the older cat talk back to her when she yowls?

Paralysis of the nicitating membrane (third eyelid) can be a result of eye infections or of systemic viral infections. There are a number of upper respiratory viruses that cats can get at shelters or while living on the streets. Feline herpesvirus (also known as feline viral rhinotracheitis) is one, and it can lead to eye inflammation and make cats vulnerable to secondary infections. Once a cat has it and recovers, it becomes dormant, and can re-emerge when the animal is under stress. If your other cat had all her vaccines and has finished the series, she should be protected from this virus (as it's part of the kitten shot series), at least.

There's also chlamydial infections (a bacteria) that can affect the eye, though they generally respond well to antibiotics. Unfortunately, there's no vaccine for this infection, and treatment can take weeks, even after the acute phase of the illness has passed.

It's also possible that there was some nerve damage that has led to this being a persistent issue, whether from an injury or from an infection she had. I had a rescued dog who always had a bit of his third eyelid showing in one eye. When we found him, he was covered with wounds and had clearly had an accident of some kind (maybe fallen from the back of a truck or been struck a glancing blow by a car, but who knows). The vet said it might have been mild Horner's Syndrome, which also affects cats and can be a result of blunt force trauma or completely idiopathic. He was otherwise healthy, had normal vision, and showed no signs of eye pain, so we finally just let it be.

I don't know about the crawling and crying thing. This could be a sign that she's uncomfortable or in pain. Eye inflammation can indeed be painful. I'd return to the vet at this point, since it looks like the eye medicine isn't working quickly, and I'd be sure to mention the crawling and crying issue.

Can you estimate how old the kitten is? It may be she's in heat, especially if she scooting on her front legs and raising with rear with her tail up.

Formerly feral kittens can be tricky, it might just be some stress from adapting to new diet, anti-parasite meds etc. Nictating membrane can just mean a bit dehydrated, not always more significant illness. One thing to check is the full range of parasites, normal meds sometimes miss things the feral have picked up from scavenging.

One of my rescue dogs had a couple of microbial infections that weren't picked up by a normal fecal test (he had persistently soft stools, though not actual diarrhea, and he was ravenous but not gaining weight). They had to do a more complicated one that looked for antibodies or something, which was expensive. But the test discovered a bacterial and a protizoal infection, and we were able to clear up the issue. Added bonus, he had some warts that disappeared as well. Those are caused by a virus, so the drugs didn't touch them directly, but his immune system was probably affected by the other infections.

She's old enough she may be in heat, which goes along with the yowling thing - and old enough to be spayed. Did you make an appt for that? Combine trips - take her in to have the eye looked at and have a blood test for the other stuff as well as a spay.

Trying for another stool sample to bring sounds like a good idea too; just watch her especially after she eats breakfast and stalk her a bit.

When you talked about the scooting and crying, the first thing I thought was she's in heat. Our kitten is just starting to go through it, though she's a little young. Heat happens whether there's a male around or not, just as human menstruation. The first couple times can be a bit gentler than she'll get later, but of course, spaying will prevent that. The first few times can be mostly being more vocal and acting a bit oddly. Scratch her at the base of her tail and see if she presents.

Oh, I missed her age. I was thinking she was younger. Yes, the weird posture and crying can definitely be a sign of coming into heat. Make sure she doesn't get out!

Do you live in a wooded type area? Chittering (what I'm guessing from your description) is often what cats do when looking at/stalking birds (and sometimes otherwise). Some of it may be a reaction to birds outside the windows, if she can see/hear them. I still think she's likely in heat, but if she was feral and lived with her mother until she was four or so months, she can hunt and that may be 'hunting' behaviour. It's no big, tons of indoor-only cats do it when they sit and watch birds from their windows.

Our kitten definitely was experiencing her first heat, but she hasn't gotten to full out yodeling yet. Mostly she is just more talkative, thank all that's holy!