This is an old issue that has suddenly popped up again and this might be the place to revisit. There are engines out there with different threads in the case as opposed to the top end. Typically what I've seen are 8mm cylinder studs with a 1.25 thread on the top, or cylinder head end and a 1.0 thread on the case end.
I have an engine on my bench right now that was a warranty return to a vendor that the original purchaser had for whatever reason, taken the head and cylinder off. He then tried to reinstall them and got the studs in wrong. He forced the course threads into the case and stripped the threads in the aluminum then tried to force the acorn nuts onto the fine threads at the top of the studs. He ruined everything and sent the engine back saying the head gasket leaked.
In short, check the threads on the studs. Some have course threads top and bottom, some have fine threads in the case and course on the top end.
Want pictures to prove it? Just ask.
Tom