Do you maybe have the redlinkserv console open in the IDE's console view?
I just did a quick test and during a normal run if I terminate the session it closes redlinkserver.exe even if I have the console open. If I click cleanup while the session is still active it doesn't kill it. The problem with it not cleaning up happens when I lose the debug probe connection, usually while I'm chasing a hard fault or something. I frequently end up in that state, but sometimes I'm able to kill everything and launch an 'attach' configuration and it'll reconnect and let me get instruction traces and memory contents, so I know the target is OK.
Back on the topic of the target audience for MCUX, how much knowledge of gdb and the ARM Cortex debug components is expected of the typical user? I'm comfortable with make and gcc and know generally how MCUX handles its managed make system and how it works with the toolchain, but I don't have the same level of experience with gdb and I don't know if it's expected. I've worked mostly with MetroWerks, Microsoft, and Borland IDEs that didn't use gdb. I could probably remember some HC11 BUFFALO monitor commands, too. :smileywink:
it might be related to having the Disassembly View open at the time you start the debug session. Is this the case for you?
Since it's still running I think you're right, that it's just a timing problem. Like the fact that it almost always brings up at least one window like this every time it starts:

If it's benign I can live with it, though the little annoyances do add up. As Erich recently pointed out on his blog, the instruction trace config requires you to close and open the view to load saved settings, and I've pointed out places in the debug configuration dialogs before where you have to click one tab and come back to another to get a button to update. None of these stop you from using the features, you just have to remember the little dance you have to do for each one.
I know there's a trouble ticket system, but is there a public issue tracking system to report and document these problems, and avoid duplicate reports? I'd rather help make the tool better if I can, than just complain about stuff that's broken.