Took the same path - updated to the latest snapshot and could no longer access hidden services, while clearnet routing worked just fine. I also route all the traffic through tor transparently.
In my case though there was no time jitter but it turned out that the 127/8 -> 127.0.0.1 route got flagged as unreachable (btw, would be thankfull for any clues on what might've caused it) and that mired the hs traffic. Enabling the route again did it for me.
