OK, I know this is very petty, but if you check out the "by developer" report in the summary screen, you will see that the rows are not coloured alternately.

The reason for this is that the colours are alternating on 'i' which is each user, whether or not they are in the project.

The way I fixed this was to initialise a counter to zero before the for loop, and then increment the counter within the if ($total_bug_count>0) {...} section. Finally, alternate_colors on this variable, as opposed to i.