Actually Wubi doesn't use the MBR to boot - it uses the windows boot
manager.
Describe in more details the symptoms you are seeing. Check the Startup
& Recovery settings (system properties, advance tab, click on settings
under Startup & Recovery). Check the timeout is not zero, and confirm
that Ubuntu is in the listed OS's.
** Changed in: wubi
Status: New => Incomplete
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https://bugs.launchpad.net/bugs/694242
Title:
Wubi does not check if Windows boots using UEFI
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