I have also seen this happen. It can easily be reproduced using the following steps (although this might not be the cause of the behavior in this specific case)
1) Open a project with no changes (fresh from teamserver, or right after a successful commit)
2) Make a change in the modeler (e.g. move a microflow step or add a widget to a page) and perform a save
3) Revert the change you just made
I suspect that it has to do with the fact that the last changed date of the project file is updated, which register as a change for svn although nothing has actually changed..
I have seen something similar before as well. If you open the .project file in an editor there is a <name>-tag which reflects your folder name(?).
If you have main line or any other branch in different folders I think that it will create the modification.
If you have turtoise svn installed you can look at the difference between the base and your changed file to see what differs.
The way the model is stored means that after certain operations the bytes of the mpr file can be different although they represent the same thing. This is nothing to worry about but we need to show a change because SVN sees a different file.