Well heres a few mistakes I have made. Just throwing these out as things NOT to do. These may or may not cause what you describe.
1: Entering 2 ships classes using the same number as below> Oh stuff like this happens not cause I am stupid
but just miss it from fatigue or typos.
Federation Fed-Cruiser2 Akira
Federation Fed-Cruiser2 Ambassador
2:Having the same hull or bridge or power hard point listed twice.
F-TRANSPORTER-II:1 B-ARMOR-II:1 instead of:
F-TRANSPORTER-II:1 B-ARMOR-II:2
3:Using a - instead of a _ in the arc entry
PrimaryHP:1:0_360:2:0-360 instead of:
PrimaryHP:1:0_360:2:0_360
4: Having an entry slid over this can be fixed by placing cursor just in front of Heavy and hitting tab. That realligns the columb.
PrimaryHP:1:0_360:2:0_360HeavyHP:12:0_360 instead of:
PrimaryHP:1:0_360:2:0_360 HeavyHP:12:0_360
5:Missing a HP entry
BridgeHP:1:2: instead of:
BridgeHP:1:2:3
6: having a weapon assigned to hardpoint 15 in DefaultLoadout.txt and not having Hardpoint 15 listed in Defaultcore.txt
Thats just a few. I imangine there are dozens of little typos/errors possible so sometimes its a bugger to find.
What I do sometimes is just start over. I might paste the lines for the Akira from both files. changing
Federation Fed-Cruiser2 Akira to
Federation Fed-Cruiser3 Ambassador
Then edit the entries from there. Sometimes its quicker than finding which columb got off.
I can do like 20 ships no problem, then I get 1 that is a bugger. Usually cause I should have just gone to bed