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.