Hi Mike, 

Some of the needles may be darker green due to genetic differences- assuming they were seed grown, and also how much light they were grown in. Any that may have been shaded by something will be a little darker.

Bare-root roots are very vulnerable to dying from desiccation so make sure you are keeping the roots damp. If they have dried out too much already, then it might be a a few weeks or longer until the needles show any damage by paling and dropping. If that does happen, they probably won't recover from that.

The discoloration or needle spotting could be  winter injury stress but we can't tell for certain. The replacement set of seedlings would probably not be any different since presumably they were all overwintered in the same area at the nursery, so it  doesn't really make sense to have them send others. 

If anything, there maybe a bit of mite damage, but that alone doesn't explain all of the symptoms. A yellowing overall needle color suggests root rot or some other systemic issue with plant health, but we suspect this is mostly environmental issues and they may recover when planted and adapted. 

There's always a risk that asymptomatic plants introduce a pest or disease to nearby natural areas, so that risk can't be completely avoided, but in this case we don't see a risk worth worrying about. 

If they are not too dried out, we say plant them and see what happens! 

Emily

you're welcome, let us know if you see other symptoms as they grow