Does sound like a phase issue, I get the same problem with my 442 filter - what have you got in the loop? If you bought it new, you could have paid a few extra $ and got a phase invert switch on your
VB-Jr, or they could probably do the mod for you.
I would be very interested in how to do the mod myself though if anyone knows how. Is it just a case of flicking the signal between two different pins of an op-amp?