Research projects (and production for that matter) is only finish after a 5-day increment (aka Production Cycle) ends. If you queue another project (research only) you will not lose any research points, as those remaining for the 5-days will be put into the new project.
As the AI plays by the same rules as you do (aside from maintenance and fuel, I think) whenever a mission ends for the AI, Aurora will stop and assign a new mission.
While only Steve can confirm it, I am pretty sure this is true.
Not sure on the SM thing. Could be it doesn´t _show_ the interrupts in non-SM-mode, but as I have it allways on, I can´t tell.