when you add checkpoints they sometimes get out of sequence therefore will not register at the proper time.
how to fix it.... go ahead and add all six checkpoints where you want them, now go to the first cp (not the start/finish line) and right click/properties, the sequence should be 0 if not change it to zero, now go to the second cp click on properties it should be set to 1 if not change it to one and so on so they are like this:
CP1 needs to be set to sequence 0
CP2 needs to be set to sequence 1
CP3 needs to be set to sequence 2
CP4 needs to be set to sequence 3
CP5 needs to be set to sequence 4
CP6 (start/finish) needs to be set to sequence 5
once you get them in order you'll be fine...
oh ya be sure all their object properties "type" is set to "checkpoint" also
[edit]
more info on cp's