ImageMagick won't ignore extra alpha channels

[mstone89]

I'm trying to convert complex, multi-layered PSDs to flattened JPEGs. If I have an image with an extra alpha channel that I've saved (as opposed to the regular RGB, R, G, & B channels that make up the PSD), the alpha channel is applied in the conversion process as a selection, and parts of the converted image are knocked out to white. The parts of the image that are knocked out to white depends on the selected and unselected areas of the extra alpha channel.

I'm not sure why IM isn't ignoring the extra channel, and is instead applying it during the conversion process. I've tried several commands to experiment with different results. Here are a few:

-alpha off: still reads extra channel and knocks out pixels to white
-flatten: doesn't maintain layer masks, grouped layers, or invisible layers (invisible layers now visible)
-alpha deactivate: same issues as above

Any insight would be greatly appreciated, thanks!

[fmw42]

Please always provide your IM version and platform. Also your exact IM command and your images.