I'm not sure how this happened, but I have a song that's 71 measures long, and X3 thinks it's 739 measures long.  (If I go to the project end arrow, that's where it goes.)  This is a a minor annoyance, except that I bounced a track without specifying length, Melodyned it, and it crashed the program, until I figured out that the, what, 40 minute length of the file was the problem.  Anyway, how can I tell X3 that this project is 71 measures?

Make sure you have no automation nodes or midi events that far out in the timeline (or anywhere else after you desired project end).

Yeah, I checked that.  There are dotted lines on the envelopes, but no nodes or midi events.

Tempo change events?
Meter/Key change events?
 
Audio clip imported and it didn't land where you think?
Where do you end up if you hit ctrl + end?

Event list ends at bar 73. Ctrl+end=bar 739.

Check if there's a node at the end of the dottet line.
If it is then try to delete it. 

Aha!  Node at the end of a buss envelope. Fixed.

I've had that happen before. Can be very frustrating!
 
I've also had tracks that I've dragged into a project that didn't land in the pane. I just assumed they didn't import, when in fact they landed WAY out in no man's land!!  LOL  ...... Go figure. The first time that happened I was totally lost, until I scrolled all the way to the end and found the "lost" track.

Clint Swank
Aha!  Node at the end of a buss envelope. Fixed.

Glad I could help