Is the machine not good in math, or were my points taken away?
Bible quote, 'be kind, one to another'
This question presents what is a formal logical fallacy: that of a false dilemma. Your account neither had points taken away nor is there a math error. The option not considered is that you've got your facts wrong.
The points you earned were association bonuses. Once you earn at least 200 points on any SE network site, you automatically get granted a new baseline rep of 100 points on all sites. This gets you past some of the new user restrictions and gives you basic privileges on all sites on the assumption that if you've figured out the basics on one site that knowledge should transfer.
Thus you earned 100 points on each of 4 sites. Your network aggregate rep will have gone up 400 but your rep on this site will only have gone up 100.
This and most other things pertaining to reputation are explained in the help center.
This page details your changes to rep, hopefully reviewing it will answer your question, if not perhaps you can be a bit more specific about what you think the problem is: