Hello Rizwan Khan ,
for dilution under 10^7 ~10^6 you need to supplement your standard aliquot with carrier DNA to prevent adsorbtion/coating of your plasmid by the eppendorf tube lining/wall.
Usually we use salmon sperm DNA that you can buy commercially.
It is also not surprising that nanodrop give you inconsistent results, its detection threshold is in the range of 10ng/µL if I remember correctly.
Good luck,
Philippe.
I agree with the nanodrop detection threshold being problematic.
Another item to consider is copy number going into each qPCR reaction. Your QPCR machine will have upper and lower limits, if you get out of that range then the data won't be linear for your curve.
The uniformity can often be improved by making "master mixes" for any given sample concentration then aliquoting into the triplicate wells.
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