When writing to an Autodesk format I keep getting a message that my template layers are being overridden and not used. What's the problem

From Fmepedia

Q) When writing to an AutoDesk format I keep getting a message that my template layers are being overridden and not used. What's the problem?

A) The message should look something like this...

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Layer 'my_layer_name' defined in template file is overridden and not used.
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There was a problem in previous builds of FME that layers were being overridden by the parameters in the Feature Type settings dialog. This was fixed in FME2005 onwards. If you're getting this message with an older build then upgrade and the issue should be resolved.