For example, I have created http://www.snibgo.org/images/gimplayers.xcf in Gimp 2.6.8. A screenshot of Gimp looks like this:
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identify gimplayers.xcf
gimplayers.xcf[0] XCF 320x200 320x200+0+0 8-bit DirectClass 21.5KB 0.016u 0:00.016
gimplayers.xcf[1] XCF 320x200 320x200+0+0 8-bit DirectClass 0.016u 0:00.016
"Convert" is consistent with 2-layers-only:
convert gimplayers.xcf -layers flatten glflat.png
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This is on Windows7, IM 6.6.2-4. Earlier versions of IM show the same behaviour.