Average calibration replicates leads to table mismatch error in MH quant

I'm using MH quant to process GC-MS data. I use a .CSV file to import my concentration levels including "reference" conc. levels to calculate accuracy values on QC's and controls. I also employ internal standards. 

After generating calibration curves I would like to average responses from replicate injections of the calibration standards. However, when I do so, the calibration tables never end up with an equal number of rows which gives the "Target and ISTD calibration tables have different number of rows" error. If I re-import my conc. levels file to "square" the tables again, the averaged responses get cleared. So, I keep ending up at this error no matter what I try. 

Is there any way to deal with this? I feel my conc. level tables will never match up with this approach. There's no way I can sit and manually inspect these tables in quant to make them match up. 

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