I would guess wubi plays tricks that the standard update fails to
consider. Depending on what computer I am working on at home, the boxes
have 3 to 5 distros on them. In updating grub2 I must boot in the last
installed distro to make any changes, that is if I want my changes to
work with the grub on next boot up. I tried updating the grub while
running in other partitions with no success, even though the conf file
was changed in that partition.

I have noticed that when I have installed with wubi, a different screen
pops up than with the standard grub screen. I had assumed that a windows
boot loader or some other loader was used rather than the standard grub2
boot loader installed when I took the time to change the partition
tables for a proper install.

It is easy enough to change the grub file to:
1.) start up using any default OS you define.
2.) limit the time that the grub splash is displayed. Where no one has
to know that another OS is installed on a machine.

Linux can take so little space, that a change on the hard drive to
accommodate a Linux distro will likely not be noticed by anyone that
allows you to install using wubi. In all likelihood, a typical windows
user has close to a heart attack just letting someone use their machine
so when they trust you enough to let you use their machine and install a
program. They would likely let you install Ubuntu the right way and
your path would be paved with much less frustration.

It is also likely that while you were not looking, there would be
another convert to the Linux brotherhood.