Success seems to vary from user to user. Let me give you my impressions. And to some extent it depends on your purpose for installing Ubuntu and what your experience level is. I will assume semi newbie for purposes of explanation thinking of future readers. I have Ubuntu installed on several computers for several reasons
First - Dual boot, with Windows being the primary OS.
I will use Ubuntu once in a while when I need or want it, or just to play around with it, but am tied to windows for some reason on this PC
I use wubi.exe to install Ubuntu as a secondary OS with no repartitioning. This is done by installing a LiveCD into a running Windows computer and running Wubi. It will do everything necessary to install Ubuntu in such a way that if I ever want to take it off the computer I just go to "Add/Remove" from the control panel and uninstall Ubuntu. It will keep windows as the first OS in the boot menu, but will create a totally "normal Ubuntu" boot other than the fact that it runs from within a container file and not from a partition. This is not a virtual machine, and not Ubuntu running "within" Windows in any sense, the performance hit from not having it's own partition is non existent in my experience. You can even use the LiveCD and gparted to put the partition back together before doing it if you want.
Second - Dual boot, with Ubuntu being the primary OS
I know I want a permanent Ubuntu installation, and only leave Windows on here for convenience and because it's already paid for, why get rid of it.
I boot from the LiveCD, and get into Ubuntu, then run the install program (or alternatively just do it from the boot menu). I let the installer do whatever it wants with regard to repartitioning and creating the proper boot settings. I have installed Windows first but have cleaned it up, backed it up, and defragged the disk.
In my recent experience there are two possible problems. The first is that you should just reinstall ubuntu and let it do the boot configuration, if you really want the separate partition and don't mind Ubuntu as the default boot (though this is probably easy enough to change in GRUB) then use the second method if you just want to try Ubuntu out then use the first.
The second potential problem is that I think 9.10 has more than it's share of problems with the install and boot areas (and I say this as someone who loves and primarily uses Ubuntu). If it were me I would install from 9.04, then update (but not upgrade) until 10.04. This is just an opinion though it is based on several actual events.