I have a similar, but not exactly the same issue. I began the game with my standard North Africa base. After about a month of selling everything recovered from my ground missions I built a second base in North America. After living space was constructed, I transfered 4 vetrans from North Africa to the new base. Then using the "start new game then load save game" trick, I hired 6 additional troops for North America. Everything is going great at this point. After another good month I start a third base in Indochina. After living quarters are built, I again use the "start new then load" trick to populate the hiring fields, and I hire 10 soldiers for Indochina. I put all the new troops into basic training, as the hangers won't be complete for awhile anyway.
Later in the month, I ran a mission from North America base on a scout I manage to take down. One of my guys, a sgt. was wounded and listed as %56 health. I didn't think much of it at the time, he'll heal up fine. But it was that "wounded" field that drew my attention to a problem.
While checking in on the Indochina base, I looked at the personnel to see how far along the training was. It was there I noticed a soldier that was wounded at %56 and still in training status (as a sgt. no less). That go me to looking, and the soldiers in the Indochina base were in fact 8 out of 10 duplicates from the North America base in name, and rank.