From my email, it looks like you get the discount as long as you submitted your primary before 9/15. See part of my email below:
"The secondary application processing fee is $50. However, I am pleased to inform you that our President has initiated a reduced application processing fee of $25 for applicants like yourself who submitted your AACOMAS application early and return the Secondary Application promptly. We want to encourage students to submit their materials early since we operate on a rolling admissions basis (see below) so please consider completing this application as soon as possible. IF YOU COMPLETE YOUR SECONDARY APPLICATION WITHIN THREE WEEKS OF RECEIPT OF THIS INVITATION YOUR SECONDARY PROCESSING FEE WILL BE $25 INSTEAD OF THE “NORMAL” $50 FEE. THIS APPLIES ONLY TO APPLICANTS, LIKE YOURSELF, WHO SUBMITTED THEIR AACOMAS APPLICATION PRIOR TO SEPTEMBER 15 AND WHO RETURN THE VCOM SECONDARY PROMPTLY. Additionally, if you haven't done so already, please be sure to get your letters of recommendation and MCAT scores to us as soon as possible as your file needs to be complete for us to review it for the next stage."