It doesn't make sense that a miswired series/ parallel switch would cause the volume knobs to "switch" orientation. If you wired the volume pots correctly, one side (one lug on the pot) should always be attached directly to ground- which could not be affected by the series/ parallel switch. If you leave the volume knob all the way down, then you should get no volume whether or not anything else is miswired- if this is not the case, then you haven't wired the volume pot to ground.
Also, the switch should be wired before the pickup selector switch and volume pots. This will mean that only one volume knob will have an effect when you are in series mode.
I can't picture it exactly, but I bet you A. just switched 2 wires on the selector switch or B. miswired one or both volume pots.
I guess you should just post a picture or just rewire it with one of the many diagrams on the internet- there are a few different ways to wire the switch by the way, but they should have the same effect.
Karl Zickrick