A semaphore is a little flag which a BookMacster Worker processes raises in your system to indicate that it is syncing bookmarks.  Workers should remove their own semaphore when they are done.  The purpose of the semaphore is to tell any later-starting BookMacster Workers that they should wait until the first process is done.  Although this is rarely necessary, it's a safety feature.

Semaphores indicate the identifier of the process which started them.  An orphaned semaphore is a semaphore indicating a process which is no longer running.  This can happen if the process or system crashed.  If I recall correctly, other BookMacster Workers will recognize the semaphore as no longer valid after an hour or so, so syncing should recover eventually.