For some reason when I place the 1st/2nd endings in place in my score using the repeat tool, the music does not repeat as written. The same process works fine with a single part but not the full score
I am not sure what version you are using, or how the score was created, I may not be of much help. I find that I have problems like this when I take an old file, then open with the new version. There always seems to be a bunch of problems.
Try clicking on the handles or squares and check the settings in the box. I don't have troubles like this when creating a new document with the latest version I have, been it seems that Finale has lot's of issues at times. The technical support used to be good, now you have email your file to them so they can figure it out. Usually takes a day or two for a responce, which is not good if you are in a hurry. In the old days, you could actually talk to a human being the same day.