[MegaTrain]

Concerning the stuck ships: I haven't seen this problem, and I assume you've checked the obvious, like they actually have engines.

Concerning the missed Messages, the only thing I can think of is a simple mistake I've made a few times:
In a previous turn, I had clicked on "Construction" or one of the other icons on the right-side of the message screen. In subsequent turns, it was STILL just showing me the Construction events, and I forgot that I had even selected it, even though I could have just clicked on ALL to see all the Messages.
It would be nice to have some sort of message history to look back upon.

Also keep in mind that for gifts or trades, you actually have to click on "Accept Gift", otherwise you don't get the stuff.

Try upgrading the game to 1.49, you may find that these problems have been addressed even if you couldn't find them in the list.