Since comprehensive reading seems too much to ask, I'll try a hands-on approach this time...(if yer willing to try this out...here's hoping...)
Open FRED and put one ship from each Shivan fighter and bomber type in. By default all ships will be placed on your map facing in the same heading

and on the same elevation plane

, that is, if you did not change the view halfway during placing these ships.
Now line up these Shivan ships, so the tip of each ship's nose is on the same grid line as it's neighbouring ship, repeat this until each one is neatly lined up.
do NOT forget to edit the Shivans and give them as initial order to 'Play dead'

and assign them to the 'Friendly' team

(unless you like the crap getting blown out of you

)
your default player ship will already be present, so nothing more to do than save the mission and load it up in FSwhichever...
now observe the positions of the ships 'in mission' and compare this to what you did in FRED...
explain...
And no, do NOT use terran ships, these do not reveal the problem...some vasudan types however do...