I have the same problem. Windows works in charset called by IONA (http://www.iona.com) as windows-1250 but Java works in the same time with Cp1250 charset. Of course, there's no perect matchin among them so some characters are not on the same place in windows-1250 and Cp1250 charsets. This mismatchin og these two caracters manifest in that way that I get "?" signs in database for characters that do not match among character sets.
In BEA WebLogic one can define character mapping between these two character sets in weblogic.xml file. Now I'd like to know where to define this character mapping for JBoss?