Well, I have never had this problem. Be sure you higligth the net before 
tracing the zone. This will tell pcbnwe that the zone belongs to that net.

I have just tried before answering and it works fine.
good luck,
Pedro.

>   I finally have all the no connections fixed, but when I fill the zone it
> avoids the traces on that layer.  When I put the cursor on a pin connected
> to the net on that inner layer it won't fill the zone.  How do I get it to
> fill over the traces on that layer?

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