Hi Michael, I've tried with my latest model and that works fine in V3 and have also tried to go back to what I thought I did but haven't managed to get it to fail again.  
 
Come to think of it the subtracted objects would have been very close to at least one surface so I expect your comment could explain what went wrong. 
 
In future I'll keep the files for you. 
 
Cheers - Jim 
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