The multiple windows issue is a programming decision.
When one window (Main AC) launches another (The chart, eRx, etc.) the programmer decides whether to make the "child" window "modal". A "modal" window means all other windows for that program remain in the background until the top most window is delealt with.
There are good reasons to do so, e.g. so as not to change patients in the "pareent window" and NOT do so in the child (there are ways around that as well that don't require modal forms)
SO it is a choice made by the programmers.