Be sure you have the 32 bit version of Office 365. Presenter is not compatible with the 64 bit version of it. Adobe is not currently showing support for Office 365 for Presenter any how, but I recall it may work with the 32 bit version.
Current tech specs for Presenter 9: http://www.adobe.com/products/presenter/tech-specs.html
I have checked PowerPoint and it is the 32 bit version, however it does not work, in fact I can't even reinstall Presenter 9 at all now, hence I've given up after some 8 tries and decided to use Camtasia Studio 8.
I find your statement about Adobe not supporting Office 365 very disturbing. What is the point of having a presentation tool like Presenter 9 and not having it work with Office 365? It is just as well that I didn't pay for it, otherwise I would require an immediate refund, I guess many others have already done so.
I have Adobe CC of which I very happy with, but I find this Presenter software completely unacceptable in terms of its ability to link with Office 365. What and when will Adobe be addressing this VERY IMPORTANT issue? Or are you suggesting we all revert back to office 2010 of older?
I am suggesting nothing, merely clarifying where this product stands in support of MS Office. While I'm glad you are not feeling out of pocket for this software, it is ALWAYS important to check the technical specifications of any application before purchasing to verify that you can meet those requirements.
Presenter is caught in a strange world between two software manufacturers, and is often at the mercy of one manufacturer changing how they do things, which is out of the control of the other. MS may have changed how PPT in Office 365 handles add-in functionality in a way that makes Presenter non-functional in it. This would result in the situation you are facing, and means that Adobe must come back and REWRITE Presenter to be able to work in the new structure of Office. This requires development, testing and validation before releasing, all of which takes time. If you need a product that works today, I suggest you try Captivate (Presenter's big brother, for lack of a better analogy) which doesn't rely on MS. Or, use Camtasia if it fits your needs.
I don't work for Adobe, and have no insight as to where Presenter is going, but I suspect it will be supported in Office 365 in the future.
Thank you for your time on this issue. Nothing has been resolved here, other than you being very open about what you think is going on, and I do appreciate that.