Hello Brian,
  I once had an older version of XWiki running with
embedded Derby under Tomcat 5
 on Windows XP.  I blew that away to start fresh with XWiki 1.0 beta 4 (still
 with embedded Derby under Tomcat 5 on Windows XP); however, I've run into
 a variety of difficulties.
 [...]
 Now the schema exists, so I start Tomcat with XWiki and try to access it.
 Now it doesn't complain about the schema not existing.  Instead it says it
 can't find the tables it wants:
    ERROR 42X05: Table 'XWIKI.XWIKIDOC' does not exist. 
  I cannot understand what it takes to have the schema
created.  Any ideas? 
Recently I've stumbled on the same problem.
After much searching, this thread gave me the answer:
http://www.archivesat.com/contact_derby-user-help/thread656404.htm
I was creating an embedded derby db with a different user than the one
hibernate used... The solution for me was very simple: use the same user and password in
both places.
Maybe this will also work for you,
Best regards,
Pablo