Since I have to wait for Haydens code/instructions to continue my work I looked at this bug and I could isolate it.
It resides in the function isDirty (line 2747 in tiny_mce_src.js). The reason is that TinyMCE doesn't clean up the generated HTML code before comparing it with the initial content.
To fix a IE-DOM bug (see here TinyMCE adds to all tags an attribute mce_serialized with an serialization ID.
An easy workaround for this bug is to change line 162 in tiny_mce_src.js to
It seems to work fine for me in IE7 but this potentially disables a bugfix for older(?) IE versions.. could someone please test this out?
Nevertheless I'll try to find another solution for this bug.