POP3 - a very old system

I am having ongoing duplication problems with about 20% of my incoming emails in my CRM email module.

Zoho Support advised that the issue was on my server side i.e not with Zoho.

However, there are no duplicates in my web email - Microsoft Exchange and Office 365. Neither is there duplication in my desktop Outlook program.

GoDaddy, my provider, said they are 99% sure that the problem lies with Zoho, and POP3. Apparently POP3 is very old technology going back to 1985. It is a known source of errors, including duplication.

Can somebody please comment, including any Zoho plans to upgrade.

Thanks