Yes. However, I spoke with several people (three guys were helping me, and, one was the dude in charge) at a real Verizon store (not sure what your carrier is, but, I know it's not Verizon at least), not a kiosk, and, I asked them that question. They said if you had a custom rom, and, put it back to factory settings, they probably would never know.
I just did a warranty replacement, and, they told me over the phone that if they found out it wasn't covered under warranty, they were going to charge me for the phone. They said to avoid that, I could go to a legitimate Verizon store and they'd check that it was indeed a warranty issue, and, set me up with a replacement. So, if what they said is true, you could go in with your phone, if they don't find that you had a custom rom in the store, you should be fine. If they do, they'll tell you on the spot and hand you your phone back. In which case you can just go to a different store and try again, haha.
Maybe your carrier has a similar policy. You can always ask at the store or call them up. Don't mention you have a custom rom though, haha.