I'm not familiar with what could cause the defect that you described, but I never expect pipe dope to be a remedy for a bad thread . If you run the threads again it may remove the problem. Also, good support of the pipe and use of the pipe holder at the back of the threader will ensure clean threads. I always go a few threads past for 1" and larger to get 11 threads and a little further with 1/2" and 3/4" to get 14 threads. You will get a better feel for it as you use the machine. Just don't go too short or too long. If you bury the pipe too deep or too shallow into the fitting, leaks are more likely. When starting the thread into the fitting my rule of thumb is at least 2 1/2 turns by hand to be sure the threads are good, before needing a pipe wrench.
By running the pipe through the die again it will not change the depth of the existing threads, but should remove defects and there is no harm in doing so. On the other side of things if you thread a pipe into a fitting, remove it, thread it in again, etc. you are in a small way over-working the threads of the fitting.They are malleable and I have experienced leaks in fitting connections from re-used fittings. It does not make me feel good to tell somebody " I told you so..." but it gets the message across when my warning is ignored and they use the fitting again anyways.
I would like to hear from others in our forum regarding threading as I'm sure there should be some fitters that could share some really good advice. Those guys really know the ins and outs of threading.