What is configuration of your CNG ? I mean which emulator and advancer you have installed ? Is "Lambda" installed ?
I also have 2005 Civic Vti oriel Prosmatic . Was having same problem with "a little jerk when shifting from lower gear to higer on CNG" and on petrol it was working fine. At that time i had emulator , PVR advancer, Landi Ranzo emulator and lambda installed.
But problem was with advancer, as these advancer generally work perfectly with manual cars but not Auto transmission.
So i got installed MAP 2 advancer/sensor and removed the PVR advancer. Problem was solved and transmission works fine now on both CNG and Petrol.