I found the solution.
alteras sopc_builder is not correct !
In the perl-file usually located in
C:\altera\quartus42\sopc_builder\bin\sopc_builder replace:
<div class='quotetop'>QUOTE </div>
--- Quote Start ---
if (! -x $javax )
{
$javax = get_java_exe($sopc_builder . "/bin/jre1.4",$shelled);
}[/b]
--- Quote End ---
by
<div class='quotetop'>QUOTE </div>
--- Quote Start ---
if (! -x $javax )
{
$javax = get_java_exe("$quartus_dir"."/bin/jre",$shelled);
}[/b]
--- Quote End ---
Open the Nios IDE shell and execute the following line
chmod +x /cygdrive/altera/quartus42/bin/jre/bin/java.exe
Now the rebuild should work.