I'm a bit late to the party, regarding the topic of the ship speed calculations, but there actually WAS a bug with the Atlas.

I have a spreadsheet that calculates everything for me, and the formula works perfectly for every ship, and includes calculations for drive tech, eradeon levels, engineer bonuses and drive augment bonuses.

Speed = ROUNDUP((BS*(1+(0.2*(DT+DE+DA))))*(1+(0.1*E)),0)

BS = Base Speed (e.g. 5,000 if Pulse < 5, otherwise 10,000)

DT = Drive Tech (e.g. Pulse 10)

DE = Drive Engineer (1 if yes, 0 if no)

DA = Drive Augment (e.g. Pulse Augment, 1 if yes, 0 if no)

E = Eradeon Level (e.g. Eradeon 10)

So, using my numbers in-game, you end up with:

Speed = ROUNDUP((10000*(1+(0.2*(10+1+0))))*(1+(0.1*10)),0) = 64,000

However, before the downtime, I actually had to manually change my spreadsheet so the base speed for the Atlas was 15,000 instead of 10,000, which resulted in:

Speed = ROUNDUP((15000*(1+(0.2*(10+1+0))))*(1+(0.1*10)),0) = 96,000

I used the same formula (minus the Eradeon multiplication, of course) for previous Universes, and the ship speeds all calculated correctly. So, in this case, BFG actually did correct a bug, rather than try to beat down the players.