One thing that I noticed between the 1000 and the 1042 is that the 1000 has the Fan integrated with the power supply, so the fan is probably run off AC. In the 1042, the fan is run off DC and as stated in the specifications greatly reducing electronic noise. It could be that your phase offset is caused by the AC fan in the 1000.
You might want to try to move everything as far away from the power supply and fan as possible (if it is possible) to see if this helps at all.
Also, the 1042 and 1000 have a 10 MHz reference signal for timing pusposes to each of the modules. The 1042 has an accuracy (skew) of 250 ps between each of the mudules. The 1000 has a skew of 1 ns, obviously much greater of an error (less accurate), which could be causing some issues as well.
I do not know what freq you are operating at, but you may be able to filter some of the 60 Hz frequencies out with a smaller capacitor 0.1uF or so.
Good luck.
Kenny
Kenny