The bolt on leads (metal O rings) can be under or over the bikes leads on the battery terminals - but I would try to fit them battery terminal, then bike cables, then tender cables... It is better to use them than the clamps - because unless they are broken they will give you a more reliable connection.
It is possible that the red and black collars on your leads are on the wrong lead - check that they come out to the same as the clamps when you have them plugged in.
It is also possible that one of the wires is broken inside from being crimped or something.
Don't leave your seat open. Mount the leads to the battery and then route the connector to where it is out of sight - but reachable from under the sidecover. I would recommend the side with the transmission so that you never ride home, park the bike, and connect a wire across a hot exhaust pipe. Don't set the charger on the seat - because it can get hot - but do something to remind you that the charger is plugged in (lay the cable over the handgrip, lay a loop of red ribbon on the handgrip or the windscreen...).
It might help to know what battery tender you are using - this is the most common...