From the documentation:

http://annovar.openbioinformatics.org/en/latest/misc/faq/

Why ANNOVAR reports T182A,T190A,T300A as the amino acid change but another web server reports only T300A?
Alternative splicing is prevalent in human genome and as a result, it is best to annotate amino acid change with respect to a certain transcript rather than gene. Other servers or software may randomly pick one script as the representative "gene" and gives one single answer. ANNOVAR tries to be comprehensive and always accompany annotation by transcript names, and it is up to the user which representative transcript they want to use or if they want to use all. There has never been a concensus in the field which transcript should be used to represent a gene when multiple transcripts are available. The most popular approach is to use the longest transcript nowadays. However, in the medical genetics field, for certain specific diseases and specific genes, there are 'canonical' transcripts that everybody uses by default for historical reasons, and you will need to manually select this canonical transcript from ANNOVAR output file to communicate with the rest of the field.

I am interested in the same thing though, so I would love to hear about any solutions others may have for this.