I saw your note on founderdating and wanted to share our experience with this. Initially our company was developing a software-based loyalty program that would be integrated directly into Micros (and other POS systems). We started with Micros and ran into the same issue with their exorbitant fees. $20,000 to apply to be a partner is a ridiculous charge and a turning point in our integration strategy.
Because of all of the hurdles, we built our own hardware that integrates into the receipt printer. This hardware sends all of the transaction information to our backend, where that data is parsed, stored and we have the capability of modifying the final printed receipt (adding graphics, QR codes, custom content or modifying the receipt template).
It wound up being a perfect solution for us because it is POS agnostic.
I don't know if this is something that could help you with your issue, but it has been a solution that comes with much less hassle than dealing with the POS companies.
Alternatively, my suggestion would be to find someone from Micros to join your board or join in an advisory position. There's a company in Austin, TabbedOut, that has navigated this space well by doing just that.
Hope this helps