Resolved this issue with the solution proposed by #5 above.

I have encountered this issue in karmic, lynx, maverick, <?>

Repeating the solution:
Copy wubildr and wubildr.mbr from your installation found in 
X:\ubuntu\winboot\wubildr onto X:\. That is, copy from the full path to the 
root of that partition. X:\ is of course the partition where you installed 
wubi. It may or may not be C:\

Verified in maverick. Had a bunch of updates after that, which asked me
to reboot. And it did fine without issues.

I am new to launchpad bug-tracking, so as of now posting this in karmic
thread (although the main reason I am now in maverick is out of hope
that probably this was fixed in later releases (including the "LTS"
lynx). But it wasn't...

Don't know whether this is appropriate place, but I wonder if it is
possible to keep the critical boot files from getting disturbed at every
kernel update? I've been using the heavyweight SUSE for 8+ years before
I switched to ubuntu recently for its "wubi" feature, because I didn't
have the patience to sit through a long installation after I upgraded my
pc.  (I keep windows to play games). But never ever did SUSE manhandle
the boot files. It is good to have updates, more so because the
lightweight ubuntu has a larger user base so is more tested on field.
But shouldn't boot files be undisturbed as long as the OS is in the pc?

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https://bugs.launchpad.net/bugs/477104

Title:
  After 9.10 grub update can not boot into Wubi install

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