I have done some testing creating a CD with Nero Burning ROM 6.6 from ubuntu-10.04-desktop-i386.iso.
As reported by nicobar in comment #48, if Disk-at-once is selected the CD is OK. Using track-at-once, the last 3 segments of 2048 bytes, which are all zero, seem not to get written and the problem occurs.
I used a hex editor to set the last few bytes of the iso to a non-zero value and burnt this to CD . Wubi copied this CD to the temporary iso successfully but then rejected it because the MD5sum was wrong.