Check if there are are mates modified during that mark. Also recalculate the motion study and check if that resolves the issue.
I'm sure there is a very logical explaination as to why this happens. I find it very frustrating and annoying. That said, If the recalculating the motion study doesn't "wipe" the leftovers from the previous run, the only way I have found is to start another study.
If you have several keys set up, you can copy and paste them into the new study.
If there are only two parts it may be quicker to delete them, run the study, then put them back in and run it again.
Thank you both. I ended up deleting the building and re-placing the same one in at the correct spot which solved the issue. When I have time I'll definitley mess around and see if I can fix it.
I accidentally had an part in a motion study in the wrong area while making the whole camera fly through and now I'm trying to move it to the correct spot for the whole video. The problem I'm having is there's these yellow marks in the motion study that keep causing it to jump back to where it initially was when I made the video. I know it's kind of hard to see, but here's a picture of what I'm talking about. (http://puu.sh/1wP6n) the building stays where I want it to be until it hits that mark, there's 2 of them in the motion study and I can't select them or anything.