KACE Product Support

I'd strongly suggest reaching out to Bit9's support team.  Typically, they either have a solution for the problem already and they just have to shuffle you to one of the support people who's implemented the solution before, or it's a situation they've never seen before and they've got to work through it.  In the former case, you can expect a fairly fast response time.  In the latter case, give them a day or two and they'll come up with a solution and get it to you.  In the most extreme cases I've dealt with, it takes a week.  They generally respond to pressure and escalate to their engineering groups in a reasonable and effective manor.

This sounds like an easy fix.  Usually a custom rule needs to be put into place, or an "Updater" rule needs to be enabled.  The big cravat, is that a HUGE weakness of Bit9 is that when you implement custom rules you have the ability to shoot yourself in to foot and basically disable all the protection Bit9 provides, so you need to know what you're doing.

(Disclosure:  I don't work for Bit9, but I know a huge number of people there.)

I am an SE for Bit9. You will probably get much more and better responses to this question on the Bit9 User Exchange. 

Contact Bit9 support to gain access to the customer forum.