Not quite clear here - are you using the same primers in all standards/? Do you have any of the standards frozen down -are the "different "plasmids different constructs eg different vectors with the same insert? or different preps of the same plasmid over time?

If you are doing qPCR then the absolute numbers should hold if expressed as copies per ng input DNA. Is your concern re the numbers generated by the standards?  i.e how do you calibrate different standards?. You may have to pick one standard as the "gold standard" and quantitate the other standards relative to that . Any differences can be compensated for. If starting a longitudinal study it is advisable to make a decent pure  plasmid stock at the start that can be returned to over time to make new standards. You may try to pick several archived preps and re-run them to see what differences you get.

Thanks a lot for your answers and suggestions.

Apart from the standards, I did not use a "validation sample" which abundance I knew in advance. I can see now that it would have helped. The problem is that I don't have any of the standards left. The same primers were used for both set of standards (338F / 518R) but the standards were prepared from different plasmids (i.e. different vectors with the same insert). This is why I am not sure if abundances, expressed as copies per ng input DNA, can be compared.  

if you have same gene insert but in different plasmids it is always preferable to linearise (restriction) the plasmid and by considering its length you can calculate the copy numbers/ng. This might differ for same standard in different plasmid. now any of these standard you can use for better comparison.

Thank you Mugdha and Julio for your answers.

If you are not confident in the quantification of your standard concentrations, you can also choose to compare only the Ct values of your 2 gene quantifications (but watch out that your threshold lines are placed at the exact same level for both qPCR run.