The CF on NanoBSD is kept read only except when the system tries to make changes it switches to RW temporarily.
I haven't seen it fail to switch to rw mode unless there was a problem with the filesystem (faulty CF, fs needs a fsck, etc).
You would need to be on either 1.2.3-RELEASE or 2.0 beta images, you shouldn't use 1.2.3-RC <x>images after the -RELEASE is out.
When in doubt, completely reflash the CF or use a different CF, and don't just do a firmware update.</x>