Did the courts actually rule that FISA didn't conflict with the 4th amendment, or did were the challenges to the law simply rejected for lack of standing to bring a challenge?
Yes. Criminal cases using evidence obtained via FISA surveillance have been challenged on 4th Amendment grounds, with motions to suppress evidence failing. I don't have case names, but if you check out In re: Sealed Case (the FISA Appeals Court decision) it lists several.