Boot-repair and Wubi

Boot-repair is a product that has appeared in the past year or so and has speedily been incorporated in community-editable support documentation (basically all Ubuntu documentation). There's no question that the author has put a lot of effort has gone into creating and maintaining Boot-repair and it has apparently been embraced as a very useful tool by the community at large.

But I wouldn't recommend it for Wubi installations and here's why...

Wubi boot problems are different
There are some key differences in the way that Wubi boots. It uses the Windows boot mangler, not the bootloader in the drive MBR to boot. So that's the first thing to check... do you actually have boot problems or is it something different?

If Windows boots okay then boot-repair is not for you
As mentioned, Wubi boots via the Windows boot manager (yes that was a deliberate typo before). So technically your computer boots okay. Boot-repair is more concerned with the boot mechanisms that occur prior to the Windows boot manager showing e.g. the bootloader (drive MBR), the boot flag, etc. So running it isn't going to help. In one case it has stopped Windows booting. To be fair to the author, the problem mentioned in that thread has apparently been fixed, but I'm not sure that boot-repair is mature enough to handle all the myriad of Windows configurations out there.

If Windows doesn't boot, then you should use Windows Repair instead
As stated before, if you do have issues with Windows, then your best bet is a Windows repair disk. Windows repair is an official Windows repair mechanism supported by Microsoft, who hopefully understand their product.

If Wubi isn't booting then probably you need to run chkdsk
This cannot be done using boot-repair, only through Windows or Windows Repair. The most popular post on this blog is all about the damaged root.disk. This is by far the most common problem with Wubi installs, and the first thing you should consider when you have issues.

What Boot-repair will do
Boot-repair detects Wubi installs and will fsck the root.disk (fsck will fix any ext4 file system damage on the virtual disk). It's not always clear to new Ubuntu users how to do this, since you need to create an Ubuntu CD/USB, boot from it, mount the partition containing the root.disk and then fsck it. There are many guides on how to do all this, but of course it's easier to have this all automated for you.

Summary
I have no doubt that boot-repair has helped many people - and there don't seem to be too many misgivings about it out there in the community. But at the same time, in my opinion, it's been incorporated too rapidly into the official documentation e.g. here without sufficient warning that the tool is not officially supported by Canonical, and in some cases, might be classified as experimental.