can't email-reply to tickets as administrator

I have two WHMCS installations, both using google apps gmail as the support mail. For the sake of discussion let's call them system1.com and system2.com.

Both are configured identically as far as I can see, using the pop.php script.

For all normal purposes it seems to work fine, customers can mail to the google apps mail accounts, the mail is imported with the pop.php scripts, no problems.

The odd thing is, I get a mail sent to the admin email account when there are tickets, and for one installation I can directly reply through email, and the reply is entering into the ticket system. For the other, the mail arrives in the google apps email account, but is never imported into the ticket system.

The util > mail log shows nothing, there are no entries for this mail.

When I run the pop.php script manually, one account comes up like this:

2$ php -q /home/system1/crons/pop.php

POP Import Log

Date: 15/08/2017 13:01:10

---

Host: pop.gmail.com

Email: support@system1.com

Mailbox is empty

---

Host: pop.gmail.com

Email: sales@system1.com

Mailbox is empty

---

The other one comes out like this:

$ php -q /home/system2/crons/pop.php

POP Import Log

Date: 15/08/2017 14:35:51

---

Host: pop.gmail.com<br>Email: support@system2.com<br>-bash-4.2$

So, 2 odd things:

1) system1 outputs in standard txt mode, system2 outputs in HTML (br tags)

2) both systems have both a sales and support email account, but whereas system1 reads both, system2 seems to crash and exit after checking the first account.

If I go to setup > support > support departments and change the order of the emails, the exact same thing happens just with the sales@ mail account.

md5sum reports same value for the two pop.php scripts - 5314ac613216da7ac7e76a7b64f87600 - so the output *ought* to be the same?

I've been digging in this for a couple of hours already and are kinda pulling my non-existing hair out. Any ideas?