Hi Cyber Calc Teacher,
I am glad you could figure out a way around the issue. This happens beacuse when you upload a PPTX file in a meeting opened in Connect addin, it (internally) gets converted to PPT before finally getting displayed to you in the form of SWF. In the other case where you face the issue, PPTX is directly converted to SWF without first getting converted to a PPT. In addition to the equations there are some other objects too that are dropped in the case which you tried 1st. You can get all the related information here: http://helpx.adobe.com/adobe-connect/kb/best-practices-sharing-pptx-files.html.
In simple language, you can understand that there are a few things that work in PPTX and there are few other objects that work in PPT. To make sure that everything(weel, almost) you have in your PPT/PPTX is displayed correctly and in the same form inside a meeting, you should use Adobe Presenter to publish your content to Adobe Connect.
Adobe Presenter is a authoring tool that comes as a Powerpoint addin. It helps you to add quizzes, videos, audios etc in your PPTX file and then publish to Connect. You can donload trial version of Presenter 9 and try your hands on that.
Thanks
Sameer Puri