One idea is to install the SoS app and take a look at the search performance tools it has in there. It'll give you a lot of information about the searches that are running slowly and you might see a clue as to what's going on.
Could you give more details such as the search string you are using? Also, have you looked in your splunkd.log for any errors or issues? I have seen some people experiencing bloom filter updates when the new install is in place on old indexes which can cause a bit of slow-down