You should protect first with Code Virtualizer and put your protector on top. Notice that Code Virtualizer adds its Virtual Machine to the last section in your application. 

For most applications, the last section is the "relocations" section and some protectors automatically remove that section, so your software protector might be deleting all your Code Virtualizer Virtual Machine.

You can try the following:

(1) In the Protection Options panel rename the last section name ("Last Section Name" option). If still doesn't work, go to step (2)

(2) In your software protection, you might find an option to avoid removing the relocations section