Are you saying that in your equipment profile that you don't have any of the boxes checked like "warm camera when sequence ends," or "park scope when sequence ends?" and it is still coming up? (there are several to choose from)
I know a lot of people including me do not want the scope to keep tracking after the sequence. I would be worried that it would hit the tripod while I'm sleeping or something.
I think it is really more of a convenience thing than anything else. A lot of times I may be shooting on one target until my main target comes up and want to switch to it when it does. In that case I don't want it to run end of sequence options so I uncheck the box and dismiss it. But after the second target is finished and it is 5am I definitely want it to run those options so as not to crash into my tripod.
Just some thoughts on it.