Ester content

Please provide more information. The QC sample -- calibrated response? Signal? Baseline? Retention time? Area? What software are you using for both the 7890 and the 8890?  Are you injecting the same standards?  ISTD?  

Yes of course:

I have injected a Round Robin to accurately have something to compare it to. Our settings are:

7890-GC

Split ratio 100 with purge 3.00 ml/min on 250 degrees celsius

ZB-WAX Plus column 30x320x0.5

8890-GC:

Same settings just a different column: HP-INNOWAX 30 x 320 x 0.25.

We use chromeleon, here are the two chromatograms beneath eachother. 

Areas for C19 are 30.6896 pA*min for the 7890-GC and 15.3801 pA*min for the 8890 so the area is double with the older GC. Here are the expected values of the RR and what we found. 

hopefully this is enough information, if not please let me know

It would help to change the scale to the second largest peak so that it does not scale to the solvent. The tiny peaks are very difficult to see.  These are both tagged as "manually integrated" as well.... Seeing the baseline, peak shape, and integration start/stop marks may be useful. 

Are any of the individual peaks acceptable and not the total?

This is a more zoomed in one, those are the biggest peaks/most important ones. 

Interesting. The top chromatogram. Peak 12 is tilted to the right and the unknown peak is not separated. Peak 14 is tilted to the right and may even be split at the top. The red baseline is difficult to see, but above the black line and not consistent on all peaks.

The lower chromatogram peak 35 - same as Peak 12 above, right? - is tilted right. The unknown at the tail is almost baseline resolved with this column/method parameters.  Peak 40 is tilted to the right  - same as peak 14 above, right?  and has a wiggle at the beginning that is hard to see.  The red baseline is difficult to see but in line with the blue baseline.

The zoomed in signal on the top one is about 525 pA and on the bottom one is about 600 pA.

See:

 5991-8706EN_37fattyacid_FAME_application.pdf (agilent.com), 

application-fatty-acid-methyl-esters-fames-8890-gc-5994-0549en-agilent.pdf

FAME Columns | Agilent

c069.pdf (agilent.com)

5991-8763EN_gc_fame_brochure.pdf (agilent.com) ..........and more.   There is a ton of information on optimizing method parameters and the way that these scientists ran the systems.

yeah its just very weird, ill have a look and thank u for ur effort and time :D