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This is about issue #4129:
https://issues.apache.org/jira/browse/SVN-4129
"predecessor links on the root node-revision skip revisions"

Symptoms:
'svn log' on a directory skips revisions in which that directory or its
children changed.
(not confirmed) 'svn blame' may skip revisions: all lines last changed in a
revision would be reported as belonging to the previous revision that touched
the file being annotated.

Occurs only in:
FSFS repositories that contain at least one svn:mergeinfo property.

Does not occur in:
Repositories that never have more than one commit-in-progress.  Examples:
Repositories written to only by 'svnadmin load' or only by 'svnsync sync'.
(This in particular applies to the slave mirrors in a "DAV Proxy" set-up.)

Fixed in:
1.6.18, 1.7.5.  The fix is server-side.

Commit-time checks preventing new instances of the issue added in:
1.6.18, 1.7.1

'svnadmin verify' support for detecting this bug added in:
1.8.0

Mitigation:
1) Upgrade to 1.6.18 or 1.7.1, to prevent new instances of the bug from
entering the history.  (1.7.5+ recommended.)
2) Either perform a dump/load cycle, or create an svnsync mirror and swap it
with the repository.  (The load or svnsync can be done with any version of svn.)