pennypooguns, sorry you're having such problems with your new old Security Six. These are really fine revolvers and normally fairly problem-free. Do you know what your gunsmith did to repair the excessive B/C gap? Knowing what was done to correct the initial problem might help troubleshoot this new problem.
I will speculate by your description you mean that when rearward trigger movement begins, either by squeezing the trigger in DA mode or by thumbing the hammer back in SA mode, it feels like something is binding and then lets go such that normal operation follows. If this is the case, your new problem is likely that the cylinder latch is not fully clearing the notch in the cylinder before the cylinder begins to rotate.
You can observe for this by looking at the latch protruding up from the frame under the cylinder while you slowly thumb back the hammer in SA mode. If the latch isn't fully clearing the notch, this is an initial timing issue and may be caused by the pawl being too long such that it engages the ejector ratchet prematurely, before the rearward trigger movement reaches the point where the latch retracts fully. That's just a guess based on speculation that the gunsmith replaced the ejector with one that had a longer ratchet hub to move the cylinder forward in the window, thereby decreasing the B/C gap. Again, just speculation but if he did replace the ejector he may not have re-fitted the pawl to the the replacement ejector ratchet properly.
Speculation as to cause aside, the symptom you describe as "difficulty" at the beginning of a cocking cycle sounds like a latch/notch bind to me and there are several possible causes besides that speculated above. If the problem is a latch/notch bind, or possibly the pawl initially binding against its frame window, I wouldn't recommend continued operation without having this repaired. Forcing a cocking cycle to happen against such a bind will cause damage to one or more parts and Six parts are getting harder to find.
I'm afraid my recommendation would be to either send it back to your gunsmith with a detailed description of the symptom you've experienced, or find a qualified revolversmith or send it Ruger. In my unsolicited opinion, this revolver should not have left your gunsmith's shop with a binding problem, regardless the cause.