You will actually want to be on Presenter 7.0.7 found here: http://www.adobe.com/cfusion/tdrc/index … =presenter. This will have improved support for PPT 10. You will need to uninstall Presenter and then run this installer. Your existing serial key will work when reinstalling.
I have run into scenarios where PPT automatically re-sizes fonts to make the text fit the text box, and then when converting with Presenter, it goes back to the larger, original font size. This has led to similar issues that you describe. You can either do a manual re-size of fonts, if this is the issue, or try publishing it locally as a zip file and then uploading the zip file to Connect and see if that resolves your issues.