I don't know if this is happening to you, but sometimes I choose the wrong directory to merge and I get this error even though all the files appear completely fine.
Example:
Merge /svn/Project/branches/some-branch/Sources to /svn/Project/trunk ---> Tree conflict
Merge /svn/Project/branches/some-branch to /svn/Project/trunk ---> OK
This might be a stupid mistake, but it's not always obvious because you think it's something more complicated.