Hi Tim

>Could you send me a screen shot of the two spectra, focussing on a copied
>peak pair and include a view if the edit assignment popup? I'm a bit
>baffled, but seeing things may help.

Here are screenshots of the situation after reproducing and cloning peaks
into an empty peak-list, respectively. The source (red) and destination
(purple) spectra are recorded with the same offset in this situation. I may
have been a bit too quick yesterday saying that the 'Edit Assignment' popup
suggests the right assignment for the reproduced peaks - sorry. 

I hope this may enlighten you.

Kaare