jabal,
The first and third reported are caused by the fact that files are overwritten with exactly the same content, or you could have made a change in a file, saved it, manually undo the change and then save again. As the file timestamp has been modified, even though it has exactly the same content as what is in the repository, it will show in compare / synchronize views. This behavior is by design.
I am filing a bug against MyEclipse, so that we avoid rewriting the .mymetadata file unless necessary.
As far as the second issue you reported, this is an Eclipse issue; you can find / report it under the Platform Product and Compare component here: https://bugs.eclipse.org/bugs/query.cgi
I tried a quick search but could not find a report describing this situation, though I have seen it from time to time in a vanilla Eclipse installation. I usually solve this by doing a “replace with > latest from head / repository” as “override and update” does not seem to remove the project from the synchronize view.
Hope this helps.