Environment:
OS: Linux Mint 14
SVN: 1.8.3
This issue occurs under command line and subclipse plugin.
I create a new java package under an existing project, and adding many classes in this package. When I commited into the branch, everything is ok. But, when I try to merge a branch into trunk, a.k.a reintegrate (don't using the --reintegrate option, it's deprecated in svn 1.8) anything wrong happened and there aren't conflict reports. Merge bring all modifications, including the new package and their files.
When I tried to commit or check for modifications (svn status), only package was shown. The files seemed like versioned, and in last revision of my repo. This fact occurs in other branches too. Every commit that includes new package has a problem to merge in working copy.
It's interesting, because when I merge the branch revision by revision, it works. It seems the problem are related with the automerge.
If when you run the command svn status shows something like this:
M .
A + your_new_directory
.. you could ran with --verbose option to see more details. Now, the output may look like this:
M rev0 rev1 author .
A + - rev1 you your_new_directory
+ - rev1 you your_new_directory/your_file
You can see more status related stuff on this question.
So, probably your files are there, but the non-verbose status from svn isn't showing.