Probably you have missed to apply the original mst when creating and/or installing Acrobat, i.e. when creating your mst-file you have to apply an additional transform (AcroPro.mst for Acrobat 6 Pro). When installing apply both transforms by the following command-line:
msiexec /i "[msifile.msi]" /[msi-switches]TRANSFORMS="org.mst;new.mst"
Example:
msiexec /i "AcroPro.msi" /qb-! TRANSFORMS="AcroPro.mst;AcroPro1.mst"
Also, you should use "Installshield Tuner 6.0.1 for Adobe Acrobat" when creating mst's for Acrobat 6 products.