Been there, but thanks for your help. I think I found out what it was. For some reason, even though I had blocked them, some of the signals were getting through to the child processes and it was acting on them as well.
What I did was to assign all the $SIG{XXX} = 'DEFAULT' then reassign what I wanted in the child and it seems to work now. This isn't a permanent fix, but it will do until I have more time to track it down.
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