It seems implants still have some sort of decimal value hidden away - I don't know how many are affected but I know that Advanced Nerves v. 2.0 says Athletics -2. In implant screen says Athletics -2... but the skill screen says -3. I can't see anything else that could account for the extra -1 penalty.
My guess is there are some decimals somewhere that are not displayed but are still in effect, and it is rounding the figures.
Same thing happened to me. My high tech skill in the implant window has evened out and states it as zero. However, on my skill screen I appear to be suffering a minus 1 malus to high tech. What gives?
I can confirm this too, decimals are still in effect.
Example:
My constructor has two imps (Advanced Nerves v. 3.0 + Special Science chip), each stating -1 malus to CON mainskill but in skill window he suffer -3 CON.
I recently installed a Hawking chip, which states -1 malus to DEX, but skill window now states -2 DEX. I have no other -DEX malus imps.
On the positive side, the bonus values also have the decimals in effect. Without decimals he should have +15 INT and +71 CST from all implants, but he is actually recieving +19 INT and +75 CST.
They removed decimals from imps, but i guess they forgot to remove them from the actual bonus-code :D