SVN Merging Via Eclipse Differs Compared to Command Line

I had some issues integrating my changes to the main repository (moving my branch into the trunk) recently and have some issues understanding why I was experiencing these issues.

Here is the exact error I was getting:

Working copy and merge source not ready for reintegration
svn: Cannot merge into a working copy that has local modifications

For what I understand, this means I have to update my branch to head and rebase with trunk before moving my branch into the trunk.

Here are the steps I performed in Eclipse:

<branch> > Team > Update to HEAD
<branch> > Team > Merge (Targeting <trunk>)
<branch> > Team > Commit...

This produced the error mentioned above.

Performing the following steps via Command Line did not cause any issues:

svn co <svn path to branch>
cd <specifically modified module of branch>
svn merge <path to branch module in trunk>
svn commit -m "<Commit message>"

Could someone help me understand why Eclipse produced these issues. I understand the steps are slightly different, but I still do not see why I should have ran into those issues.

Additionally let me know if any of my terminology is wrong and needs any correcting or further explanation. Any and all constructive criticism appreciated.