I worked the exact same issue last night with UA - had to book separate PNR's for my wife and I to use separate e-certs several weeks ago. The problem I ran into was that I kept getting bumped up to E+ automatically and my wife did not. I called UA res last night, explained the situation, and asked that she tie our PNR's together, move my wife up to an E+ seat, and if possible put my wife on the UDU list with me. She put me on hold, came back 5 min later, and was able to do all three. We are now in E+ together and if I get upgraded she comes with me since our PNR's are linked.

I have actually encountered a similar situation several times in the past when I flew on a revenue ticket and my wife flew on miles. Every time I was able to link the PNR's and move her to E+ with me. About half the time when I call the agent tells me thy can't do this. I usually call back, explain that I have done it in the past and ask them to try. It takes a bit longer since they have to manually link the reservations but it is certainly possible and has been done many times.

Try again...Good luck