To measure acetic acid by GC and from a pharmaceutical product matrix is not trivial.
The fact that you are getting a peak at all at low levels is commendable.
Any active site on your column, detector, or in your injection port will cause absorption of the acetic acid. Replacement of your injection liner often and use of the proper phase for your column will improve your analysis.
Acetic acid is usually done by ion chromatography or by HPLC.
There are many published methods and companies that sell HPLC columns that will be happy to assist you.
best wishes,
Rod