My paper got accepted for a conference. Before submitting the paper, I used Turntin to check for any similarity and found only 6%. But after the conference reviewed my paper and sent it to me, I again checked for similarity (as I made some changes) and found that it was 95% similar! 90% of those come from a student paper at a Texas university. Why is that? I have to submit the final version tomorrow. Is this going to be any problem?
I don't see how any of us can say. Maybe you stole it from a student at a Texas university. Maybe they stole it from you. Maybe a glitch. Maybe the conference will use a plagiarism checker like the one you used, maybe not.
You should never need to check anything you've written yourself on a plagiarism checker, because if you wrote it yourself you don't need to check it for plagiarism: it isn't plagiarized if you didn't plagiarize it, regardless of what a computer comparison says. Focus on not plagiarizing, rather than focusing on making sure you can evade the detection system; evading the system of checks is something for guilty people to do, not honest ones.
In some cases, sending a copy of your work to a plagiarism detector may result in it showing up as plagiarism later, because the plagiarism software works by making comparisons to previous submissions.
There's a plethora of reasons this could have happened but, assuming the conference did not make any mistakes in the paper that was checked and who it was reported to. It may be that turnitin added your paper to their database after you submitted it and afterwards when the conference went to scan your paper turnitin recognized your paper as previously submitted. I would bring this up to the conference and try to show them as much documentation you can (i.e. timestamps on browser history, any editing history assuming your text editor supports this).