We have provided a fix for these issues in version 1.0.10, released today (10th May).
It should fix many of the issues you were seeing with elements being removed from the HTML. Multiple empty paragraphs are still collapsed into a single paragraph but that seems to be a feature of HTML rather than the editor (the multiple paragraphs still exist, they just aren't appearing as such).
We are going to look into more improvements to TinyMCE over the next few weeks.
Simon