Here is the situation:

1) Questions created in 1.9 or earlier.
2) Upgrade to Moodle 2.0
3) Question has new features in 2.0 that didn't exist before and now have defaults set for new question features
4) Regrade is done (lets say if a student has to make up a quiz and they do it after site is upgraded to 2.0)
5) Regrade applies new question default values and changes marks for all other students.

Here is a specific example:
1) A calculated question was made that did NOT include a graded unit. Students were given specific instructions to NOT include units and those that ignored the request did receive a penalty.
2) Upgrade to 2.0 was done (not on a production server, but on a copy of the production server)
3) A dry run regrade was done just to test the new feature
4) 171 out of 194 quizzes showed an increase in overall marks.
5) Looking at the questions that were specifically affected it became apparent that the new calculated question type included a separate unit handler that graded the units separately from the numeric answer. The default is DO NOT GRADE UNITS.
6) Any student who had put a unit had the penalty removed by the default causing an increase in their marks for that question.

This only affects upgraded question types that have defaults associated with how the question is graded that don't exist in older versions.

Discussion was originally started here: http://moodle.org/mod/forum/discuss.php?d=159150#p697060