Jonas MeyerJonas Meyer has the right of it. Comment flags have actually never been shown in the flag report (among other things, any valid comment flags would not be possible to show because we do not retain visible traces for normal users to see deleted comments like we do deleted posts). However, at the beginning, they did affect flag weight by half the amount - +5 for a valid, -5 for an invalid.
Unlike reputation, flag weight is simply calculated as an operation performed on the current value. We lack any form of state history for the flag weight value, and with it the ability to track exact sources of the change. As a consequence, there are some users who have positive or negative flag weight changes from comment flags that are retained from when that period occurred.
The user in question has, apparently, had -25 net result from comment flags prior to the flag weight changes.