The key may be in the fact that you did the same thing I did - replaced original designed actuators with Pacific Rim repro c _ _ p - don't get me started.
When I did the same thing back in the summer of 2004, my new, repro actuators (acquired from Classic Industries) had two problems. 1) the vacuum connection on the actuators wrere not oriented the same as the originals, which caused an interference issue between the vacuum connection on the back side of the cannister and the mounting bracket - relaitively minor, but still a nuisance that had to be dealt with.
Secondy, my headlight doors did exactly the same thing - they stayed closed when the light switch was pulled all the way out and the lights were on and they were open when the light switch was pushed in all the way and the lights were in the off position. I wasted the better part of an afternoon chasing the vacuum connections at the light switch, at the relay valve, and then it occurred to me to swap the vacuum lines on the actuators and connect the red stripe line to the back (instead of to the front) and connect the green striped line to the front (instead of the back) of the actuator. You could accomplish the same thing at the relay valve, but then to the astute eye it would be obvious that, per the Assembly Manual, this was not the way Chevy (Norwood) originally built it.
Bottom line is that the actuators, at least the two that I got, operate bass ackwards. Go figure.
Run a little experiment, swap the vacuum lines at the actuators - I'll bet your relay valve is ok.
Attached Word document is a pretty good guide to the system, diagrams, etc.