Buddy had round worm VERY bad when I got him, ( I THINK it was round worm) and it took months of treatment to get rid of them all. But some types of worms stay dormant and will resurface after treatment and/or a negative.
So she may have had worms... the shelter dewormed her... but maybe there back again. Who knows.
Like the others said, a stool sample to the vet will help.

Even though it's been almost a year since Buddy's first negative stool came back, I still take samples in a few times a year. The earlier you catch the worms, the easier it is to get rid of them.

Buddy's was never in pain or anything like that, just had soft stool all the time and never gained weight till the worms were gone!