Hello,
This is a very common issue, and not sorted by M2E Pro till date, no need to use the M2 editor, rather just copy and paste the template in plain text, and once transmitted to eBay it should be all okay, another thing as I just noticed, eBay does not allow any sort of scripts, just make sure to strip it from the template, and if you want to edit the template, do it off-M2E Pro altogether.
I have over 10 years of experience in eCommerce Development and over 7 years in Magento.
Looking forward to hearing from you.
Sincerely,
Ibrahim Saleh