glitches in publishing from powerpoint

We are in the process of putting together a huge e-learning project of >200 15min presentations.  We received our first two presentations and both contained glitches when publishing from powerpoint to the web.  The first glitch has an animation that involves a color change.  The color never changes except at the border.  This animation plays perfectly in powerpoint.  In the second presentation, there are many equations written with microsoft words's equation editor and several of them show up as nonsense in the published version.  I need to communicate a fix to our developers before we receive the bulk of the project.  I would appreciate any suggestions.

Thanks So Much

Ross