Why can't I boot Xubuntu 12.04 when I install it to my flash drive with wubi? It works just fine when I install it with UNetBootin but not with Wubi. When I try to boot from the flash drive, it says "Missing operating system"
Wubi boots via the Windows Boot Manager and
grub4dos. The place you install Wubi, whether the
D: partition or an external USB partition doesn't matter. It's not bootable without a boot manager.
By booting from the USB, your BIOS is checking for a bootloader in the Master boot record, and this is not something Wubi will ever add.
What you need to do, is boot Windows normally with the USB plugged in, and then select Xubuntu from the Windows boot manager and
wubildr.mbr) should find Grub 2 (in the
wubildr) and then locate the Xubuntu
root.disk and load it from the USB.