Hmm missed the colour thingie of the weapons itself
The problem itself, you don't really see that your Mo-ship has two capital weapon slots, seams like they were running out of RGB colours
(and just a sidenote...don't buy the cheap ones, at the time you'll have to fight the big guys it does matter if your gun hits for 400-600 or 1600. I don't want to spoiler you which way you've to take but there are ships ...hmm alás they just can drink coffee while you think your guns do damage ^^..it's sometimes cheaper just hiring some mercs, they do great)
But if you use the jump-from-mission-to-mission-system, it partly doesn't matter at the beginning, but you'll see