Too long for comment, sorry
I can't catch your case, because (for extremely degenerated test)
>svn log -v
------------------------------------------------------------------------
r4 | Badger | 2014-06-30 00:10:03 +0600 (Пн, 30 июн 2014) | 1 line
Changed paths:
A /branches/F1/B.txt
A /branches/F1/C.txt
Added B.txt + C.txt
------------------------------------------------------------------------
r3 | Badger | 2014-06-30 00:08:26 +0600 (Пн, 30 июн 2014) | 1 line
Changed paths:
A /branches/F1 (from /trunk:2)
Branching trunk into F1
------------------------------------------------------------------------
r2 | Badger | 2014-06-30 00:07:09 +0600 (Пн, 30 июн 2014) | 1 line
Changed paths:
A /trunk/A.txt
Initial data
------------------------------------------------------------------------
r1 | Badger | 2014-06-30 00:05:33 +0600 (Пн, 30 июн 2014) | 1 line
Changed paths:
A /branches
A /tags
A /trunk
Imported folder structure
------------------------------------------------------------------------
merging F1 into trunk must not and does not produce unexpected tree conficts
trunk>svn merge file:///Z:/Repo/branches/F1 . --dry-run
--- Merging r3 through r4 into '.':
A B.txt
A C.txt
for
>svn --version
svn, version 1.8.9 (r1591380)
compiled May 5 2014, 22:12:10 on x86-microsoft-windows
and must be the same even for SVN 1.6+