+/- speed is not a percentage value. +/-10 speed is +/- 1 real speed.
I'm tempted to assume you're playing either DA or DL since you reference a base speed of 1-in TA the base speed is 2. If you are indeed playing TA, as your most recent post seems to suggest, then you need to find two things-whatever is causing the discrepancy between the 2 speed your modded core ships should be and the 3 speed they are showing up as-and secondly, how you are managing to see 1 speed ships in the first place, since TA's base speed is 2.
To which I would ask, have you actually built any new ships, or were you simply looking at the ships you've built in the shipyard? The shipyard's shown speed and range are not quite correct-range is modified by map size, while speed fails to account for racial bonuses. In addition, the shipyard shown speed does not seem to recognize a base speed as such, which wasn't a problem in DL/DA where base was equal to minimum, but will result in TA ships showing up 1 speed slower in the shipyard than in game (with no racial bonuses, even).
I haven't personally tried modding the default ships but I see no reason why their speed would be "fixed"-they are to my knowledge not unique in any sense. The components for the starting ships -might- be fixed, though, which would result in an apparent speed fix as well.
Ships move at 1pc/wk when moving off of an asteroid field. The following turn, they are restored to full speed.
Minimum speed is 1, so you can't have a ship that moves 0pc/wk. (We call those starbases, actually, and you can't put engines on them.)
For what it's worth, I don't see more than a cursory mention of the flagship. In the above scenarios, it is 4 speed, yes? And have you or have you not modded it as well?