In this score I have, as always, selected the designated first time bars, hit "L" and selected "1st Ending". A beautifully placed 1st time bar line appears over the bar, ending nicely at the repeat barline as it should, aligned all the way down the score in each instrument.
However its appearance in the extracted parts varies greatly to the extent that in some parts, it keeps going clear off the page (see attach). I don't know if it has anything to do with the multirest, but of course there isn't one in the score, but FWIW, I tried Layout>show multirests but toggling that in the part didn't make a difference.
The square handle on the right edge isn't actually grabbable and just results in a hand icon moving the whole page around. I can eventually fix it after much mouse gymnastics grabbing the left hand edge of the line and it eventually starts to move and if I go crazy enough the right edge nudges onto the next system, then I can do the same process again with the right edge to eventually get it where is should, then I go and fix the 2nd time barline that gets messed up.
There must be a simple fix to save me manually "fixing" this on all the parts, but I can't find it
Without seeing the actual sib file, I suggest you cancel the system break under the 1st ending box. Then you should be able to pull the box end handle back to its proper position. Failing that, make a temporary system break at bar 126 and try again. Failing that, post the sib file for inspection. My only other guess is that the box end is badly placed in the full score.
Just before I attached the sib file, I had another look at the score itself and the line actually wasn't quite to the repeat bar, so I just deleted and redid it in the score and it's now behaving in the parts.
I've attached the "pre-fixed" file in any case. Not sure what happened the first time I added the line. The part I screenshotted in the OP was flute 2