Nobody is ever going to read the FAQ pages anyway.
OK, small attempt at humour.
In the XML files you will find a VISABILITY= section for each program entry. Remove this & they will always be usable in the menu, regardless of wiether or not they are of any value when running from PE.
EXAMPLE...
CODE
<!-- Nu2Menu entry for HijackThis -->
<NU2MENU>
<MENU ID="Programs">
<MITEM TYPE="POPUP" MENUID="Malware Tools">Malware Tools</MITEM>
</MENU>
<MENU ID="Malware Tools">
<MITEM TYPE="ITEM" CMD="RUN" VISIBILITY="@FileExists(@GetWinDir()\setupldr.bin)" FUNC="@GetProgramDrive()\Programs\HijackThis\hijackthis.exe">HijackThis</MITEM>
</MENU>
</NU2MENU>
Would be changed to...
CODE
<!-- Nu2Menu entry for HijackThis -->
<NU2MENU>
<MENU ID="Programs">
<MITEM TYPE="POPUP" MENUID="Malware Tools">Malware Tools</MITEM>
</MENU>
<MENU ID="Malware Tools">
<MITEM TYPE="ITEM" CMD="RUN" FUNC="@GetProgramDrive()\Programs\HijackThis\hijackthis.exe">HijackThis</MITEM>
</MENU>
</NU2MENU>