Doesn't have to be port scanning per se, just a rogue program will do the trick as well -- I once had a MySQL GUI which could connect to a host via an SSH tunnel but the host would ban me every so often when I did this.
It's probably a rule in iptables, if so you/they should add a rule somewhere above that throttling rule that whitelists all data from the IP(s) you guys are connecting from.
To see all iptable rules:
iptables -L -n --line-numbers
To whitelist your IP
iptables -I INPUT <n> -s <YOUR IP> -j ACCEPT
Where <n> is a number lower than the throttling rule (most of the time this is the last rule of the chain).