Couple of things that can adversely affect how Windows Defender Offline performs.
1. It's absolutely necessary that the bootable media is created on a malware-free computer. Otherwise, the malware could prevent your PC from downloading the program, burning it correctly to the bootable media, or prevent it from operating as intended.
2. Do not re-use a previously created a CD or DVD.
This tutorial gives some more info about creating and using the bootable WDO media.
Windows Defender Offline