stlhdr got it.. maybe I wasn't very clear about this the reason there are 2 distinct runs is because when hatchery fish spawn in the wild they produce nothing
the progeny do not survive therefore any interactions between hatchery and wild fish result in no returning adults. If no offspring of a wild/hatchery return to spawn then there is no contribution to the gene pool therefore no altered genetics and the two strains remain seperate.

It doesn't seem to matter where the hatchery strain comes from. This same problem has been documented in 1st generation wild broodstock planted back onto the same system.