Once again, the denizens of the forum are right, and Dan is wrong.
Two things happened:
(1) I applied rounding to the tractor beams AFTER applying the (Arcs + 1) multiplier, not before. This is incorrect according to the Core Rulebook (although I have to wonder if the rule should be changed, particularly in the case of really small base SU values).
(2) Early on, probes were going to be seekers, and so a DRAT was included in the spreadsheet I was using. However, after I found out they are direct-fire weapons in SFB/FC, I changed them to direct-fire weapons in Starmada -- but for some reason neglected to remove the DRAT from the spreadsheet.
The bad news is that all of the ships in KA are point-costed incorrectly. The good news is that the difference is VERY minor... a net change of -2.2%. The biggest change is -13 points (the Battle Station goes from 813 to 800 points). And since all the ships are reduced in cost, the relative change is even smaller.
After careful consideration, I'm not going to worry about it. Yes, the values are "wrong", and yes, it's frustrating to those of you trying to recreate the ships on your own -- but in terms of game balance, it's really a non-issue. However, remind me to run the ships from Romulan Armada by you guys first...