changing stuff midstream isn't such a good idea, make sure to change it before the playoffs at least.
you should be able to maually schedule playoff games - as long as still between calendar events "plagoffs begin / end"
things don't get messed up in the playoffs, they get setup in a way that doesn't work

so, don't make a playoff system that isn't 2-4-8-16-32-64.. etc unless you incorporate byes and such. this stuff doesn't just srping itself on you without warning, it is planned out ahead of time -- whehter good or bad setup.
i use a custom schedule every year - same one - nfl-style with top 2 teams getting a bye, but only 6/30 teams make it (3 10t divisions that only play within division, best 2 divisions winners get a bye first round, all works well)