Got there in the end.
Several things caught me out.
First, dirty test environment.
I wasnt making sure that any processes started during testing were killed.
Stupid mistake by me caused some confusion while trying to work out what was happening.
Of course this shouldnt be able to happen if the pid files worked correctly. see Second point
Second, pid files part 1
The skeleton bash script in init.d doesnt make it clear that pid files arnt created by start-stop-daemon when you give it the path to the pid file. You have to make sure that you set --make-pidfile to create the pid file or it assumes your service/daemon creates the pid file.
Third, pid files part 2
When start-stop-daemon is called with --make-pidfile, it doesnt know anything about any forking within your service/script. It creates the pid file with the pid before forking. So any further calls of start-stop-daemon wont work as the pid file is not associated with the forked process.
As I said got there in the end, just need to put the logic into my perl service/daemon to handle the pid file and locking rather than relying on the init.d script and start-stop-daemon as I assumed you could.
Hopefully if someone else tries something like this, the above will help
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