An issue was identified with the Reputation system and this has been corrected now. There were number of small issues that over time made a larger problem.

These have all been corrected now. There is a strong chance that most members will see an increase in their reputation because of this correction and there is a slight chance that a few people will see a decrease. Either way, the values are now correct and should be correct going forward.

Thanks to @HelterSkeleton to pointing out the issue and helping to locate the causes of the issues.