I don't know if this will have any bearing on your problem but I've got the RRA 9mm upper with the 9mm buffer and hammer but on a semi-auto lower and started have short cycle problems. Seems I decided to try a thin coat of grease on the bolt instead of the CLP because under rapid fire I would get a lot of vapor/smoke from the charging handle gap and it would get on my shooting glasses. I have 1500/2000 rounds throught the gun, nothing else was changed and the darn thing started short cycling to the point the fired cartridge would not eject fully and get jammed in the receiver. I cleaned all the grease out of the receiver and bolt, soaked the thing in CLP like I normally would do and and the rifle went right back to shooting like a champ. The point is The grease was slowing the bolt because it was stickey and thick. I was wondering if the new buffer tube might have enough drag to slow the buffer down and cause the short cycle. Are you using your first buffer and spring or a new buffer and spring from RRA? Try cleaning the buffer tube, spring and buffer with solvent and see if this helps. I didn't notice any difference in the operation when I pulled back on the charge handle either when I had my problem.
By the way, I shoot only the cheap stuff from WalMart, the 100 rounds in a box for $11 stuff so this is not high power stuff.