Hello Wagner, I like to improvise over a looped background as you do (I'm a sax player), so I hope I can help. I don't know whether you have Band-in-a-box as well, but if so I would recommend it as a practice tool over RealBand; there is greater flexibility available with it.
To possibly fix the 'cracking' problem, I can only think that you might examine carefully the data on the tracks at the beginning of the loop (perhaps play each track by itself with the others muted to see whether it's to do with a particular track)and if so, delete the offending note to perhaps fix the 'crack'. This is just a guess and might be way off the mark. Good luck with your problem.