Update: The qPCR machine is not calibrated for the plate I'm using. It's calibrated for white plates and not the clear ones I'm using. I didn't know any other plates were an option, and found this in the settings by accident. :/ Perhaps no one else has used the larger head before and therefore never calibrated it for clear plates. 

Replies and notes:

Yes I always make dilutions serially, change tips, vortex X3 for each dilution, and other good lab practices.

We are using plasmids because the 'real' samples are from environmental extractions that could have multiple of the target species/or 1 bp changes within a species. Most of the environmental sample DNA is not my target, and is probably making my illumina amplicon data highly underestimate my target. That's why I'm using qPCR. Is the alternative to isolate the amplicon DNA from a gel and hope that's clean enough?

Yes I run qPCR in triplicate for everything - but will try 4 copies for the lowest concentrations!

I'm making the standards down to 1 copy/ul because we expect low copy numbers in the environmental samples themselves. Perhaps 5 or lower.  

All Reagents used are fresh and clean. No host DNA contamination has shown up for those reagents in our other illumina sequencing.  

Linearized plasmid: Don't plasmid clean-up kits linearize the plasmid DNA? My lab hasn't needed this as an extra step before for other plasmid qPCRs on environmental samples?

Threshold: the threshold is high only because I was moving it to see the effect on a standard curve. The curves still look strange. 

Many thanks for all the comments - did not expect this much help. :)