I've found a solution for my problem.
The problem is the action attribute of the forms which are used for the upload.
PrettyFaces changes the action attribute to the new pretty-url.
If you change the action attribute to the real url (the one with .xhtml,.jsf,...) the fileupload works again and the allowCasualMultipartParsing="true" entry in the context-file(tomcat) is not needed anymore.
To change the path place this script into the view (your xhtml-file; jquery needed):
Now the fileupload is working for all of my files including the ones which not worked (even with allowCasualMultipartParsing="true" solution).
Tested with Primefaces4.0 FileUpload-Component.
EDIT:
Is there any other better solution?
