I solved my problem. I'll describe the solution here, maybe this can help someone in the future.
First, my setup.
In my pfSense box, I do have a MultiWan setup with two independent links. Since my ISP gateways do not answer ping requests, I have set Google's DNS IPs 8.8.8.8 and 8.8.4.4 to monitor my links.
And the problem:
Apparently, all my ISP links were intermittent for international hosts (Google's DNS is an internation host for me, since I am in Brazil).
Due to this, all my links became unstable. The %loss in Status > Gateways were very high (like 30-40% of loss on both links). This was clearly affecting several pfSense services, like SSH and my users' internet access.
There were also some lines stating this issue in the logs:
/rc.start_packages: Gateways status could not be determined, considering all as up/active. (Group: MultiWAN)
...
/rc.filter_configure_sync: Gateways status could not be determined, considering all as up/active. (Group: MultiWAN)
...
/rc.openvpn: Gateways status could not be determined, considering all as up/active. (Group: MultiWAN)
Since there's nothing I can do to solve the intermittency of my ISPs link, I decided to change the monitor IP of my Gateways (in System > Routing > Gateways) to an IP that wasn't intermittent (just to cite, I changed them to www.uol.com.br IPs, 200.221.2.45 and 200.147.67.142).
This immediately solved the problem.