So, the eventual cygcheck output reveals that the problem is this:
http://cygwin.com/ml/cygwin/2003-09/msg00569.html
Which should be fixed in tonight's snapshot.
Ah, duh. Sorry I should have thought of that. I guess I have sufficiently hidden the fact that my home directory is on a mount point! Even from myself :-)
Actually I'm not sure if I would have made the connection - I do vaguely recall something about .lnk's showing up on network paths.
Thanks for the quick diagnosis and impending fix.
=== Obligatory witty saying: Bad command. Bad, bad command! Sit! Stay! Staaay..
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