I think I just solved it - a "well DUH" moment because it was
staring right at me while I wrote my previous post. Your screen
shot shows that the offending layer is a float, not a "normal"
layer. Click the anchor button in the layers tab (if there is a
"real" layer under the float) or the new layer button, and
everything should suddenly get normal. I am not sure this accounts
for the whole problem but I have at least partially reproduced the
symptoms here, i.e. the "Flatten Layer" command is grayed out when
there is a "float" present.
If that don't fix it, let us play with the original image file...
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