Most probably, you have just a lot of files inside Virtual Box, right?
To check if this is an issue Enigma Protector that applies additional protection to virtual files, try to pack same exe with our freeware solution Enigma Virtual Box. Will it work faster or no? If file will work faster with Enigma Virtual Box, then the issue belongs to Enigma Protector, to the additional protection that it applies. If the issue will remain even with Enigma Virtual Box then this is an issue of virtualization at all, and some other methods need to be applied to fix.
So waiting your reply about Enigma Virtual Box.