Hi,
we had some discussions during the dev meeting regarding hidden services and why users sometimes report that the access to them fails. The general problem might be that the specific hidden service doesn't exist anymore. However in some cases the HS exists (see URL:http://tor.stackexchange.com/q/1442/88 as an example).
So one theory was that the transistion from TAP to ntor might cause problems. I tried to test it and found no evidence so far.
What did I do? I checked out the current Tor source from git and the tor-0.2.3.25 tagged version. I built both versions and gave them a minimal torrc (SocksPort, Log, DataDir, ControlPort). After the Tor process built a circuit I used a random page from the hidden wiki and tried to access it. If it failed, I tried either the HS from TorProject or DDG. If it succeeded, I built a new circuit and tried another HS.
During the first tests I used the hotel network, which was kind of flaky. With a more stable connection I tested nearly 20 hidden services and found no difference in the behaviour of both Tor versions. Both failed on one random HS and opened all other reasonably fast.
While this is no final proof it is good evidence that there is no connection between failing hidden services and TAP/ntor. So maybe we need another theory to test. ;)