[i]So I guess, I have misconfigured something in zpSkeleton theme.[/i]
Only gjr can answer if his theme uses hardcoded thumb sizes for layout reasons, so not necessarily configurable at all.
[i]But on the admin side, the Albums > Images page still show the default cropping thumbnail, not the custum cropping, even after refreshing the page...[/i]
The admin side does not really matte, for layout reasons the custom crops are not used there (I think, don't remember right now).