Did you change any tweaks? There are two tweaks that are for collections on SONY ereaders. One has two options for the names of the collections.
Also, when you copied the library over to the new computer, did you copy the contents of the calibre configuration directory, or just the library? The last time I did this, I copied the directory over after installing calibre and it saved me redoing all the configuration and reinstalling the plugins. I'm not sure if it is a Kovid approved method, but if it works...
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