A resposta está no guia do Wubi:
Posso forçar o Wubi a baixar e instalar uma versão de 32 bits do Ubuntu?
Yes: either pre-download the appropriate 32 bit ISO manually and place it in the same folder as Wubi.exe or start Wubi with the "--32bit" argument.
To modify arguments, right-click Wubi.exe and select "Create Shortcut". Then right-click the shortcut, select Properties, and modify the Target line, for example: "C:\Documents and Settings\Desktop\wubi.exe" --32bit