The problem has been solved, but I thought it was a bit wierd and figured that someone else may encounter it. If so, maybe this little post will help. Here is the problem and how I fixed it:
I recently encountered a problem (late on day 180 and early day 181 before 0900) , every time I clicked on "enter cockpit" I would see the "server down" message screen. I know travel was working fine, and all other functions of the game were also working. I also went into mIRC and asked anround, and no one else was having the problem so I took a guess that it was some kind of trouble with my browser, IE6, and I upgraded to IE7. This seems to have fixed the problem.
I did both of those things Syn, and they did not help. The screen only displayed properly after I upgraded my browser. Maybe there was something else wrong with my system, but in any case upgrading the browser fixed the problem.