Two problems with --only mode:

1) On the master, the "finding start" mode scanning doesn't work correctly when an "ns" field is specified in the oplog query.
2) On the slave, when a fresh slave is created the last oplog entry is saved for syncedTo regardless of the ns for that op.

These issues have been addressed in the v1.2 branch with
de365ac8eb96572003bd158d098916272b68eb75
1d82d20390804309258cd6d8fffd7f62c4accce6

The --only option should not be used unless both master and slave have the fix in place.