We've had a similar issue ever since 9.0, and in our case, it was only users on 5540 IP consoles, which for us, is only our reception department. (8 consoles)
We're actually in the middle of moving them from the 5540 consoles to the MiVoice Business Console soft console, and that does not seem to have the same issue.
I asked our VAR about the issue several times, and at the end of they day they couldn't fix it, had never heard of it, and went as far as saying we were their only customer that had more than one hardware console. Everybody else, apparently, was using regular sets or MVBC.