I've noticed in the past that putting spaces within the fields of the shiplist can cause ships to start missions in the D2 in a damaged state. This is hard to spot, since these spaces will be mostly invisible in excel or text editors. Shipedit makes this mistake easy make, as it is really simple to forget yourself and clear one of the fields by hitting the space bar instead of the delete key
I've spotted the following ships in your shiplist having erroneous space characters. (There may be more; I did a cursory search.) To find the spaces, open your shiplist in Word and turn on the paragraph markings.
F-CF
G-MON
K-E5K
K-E7
K-FD7
K-FD7K
K-B8
K-WG2
K-WG2+
K-WE4
K-WE4+
L-DAxPFT
R-SHR
I don't know if these correspond to any ships you've been having trouble with, or what if any trouble they will cause. (Inserting spaces doesn't always cause problems; seems to depend upon where the space is inserted.) But you might want to check this with your trouble ships.
I played on LB3 for a while tonight and had fun. The 3 on 3 missions seem to be working perfectly, and the mission-matching was right on. Good work! I look forward to more.
-S'Cipio