ah, hadn't experienced this. I too usually sim the CPU picks one by one. Or at least I tried to. Even doing that, it seemed like the system got confused. I was simming up until the point where the system kind of just sat there, and when it wouldn't sim anymore. The next team would be on the clock and use the full 2 minutes then select. But after that point it's all downhill. It'll say such and such a team is on the clock but that team picked 5 picks ago.
Im aware that the clock runs continuously no matter where you are. I'm sayin I'm on the clock... i've got 2 minutes to select a player. I'm on the screen to select a player and BOOM.. i find one. I try to select him. So i click X or whatever the appropriate button is. System prompts me that I took too long and that the CPU has made a selection for me. I'll go back and look at the clock and I still have well over a minute left to select.
The first time yes.. It was a traded pick. But I simmed through 2 other seasons just to draft and it was the same issue, just without trading. The only way I could select a player was literally if I went in and selected a player within 10 seconds of accessing the players available screen.