Yes you can dock at any allied port to re-fit and re-fuel but you have to dock at your 'home' port to complete the tour.
The game often changes home ports and either forgets to tell you or it gets covered up in other message spam.
As said above look for the tilted anchor.
The crash is another matter Im not sure why it would crash when entering a port unless its trying to load and object/sound file which is corrupted.
Short of a re-install I dont know how to help you.
About the re-install even that has a few twists and turns here is a good thread on the topic
http://www.subsim.com/radioroom/showthread.php?t=133290