“Allow Multiple Instances” is a new function as of v2014.1.0.15 that allows you to run multiple copies of the software, each with it’s own set of Settings, Users/Groups. This is very useful for organizations which provide ftp-services for their clients and would like to keep the groups of ftp-users in their own separate instance.
It’s also very useful for controlling bandwidth used by each instances, as multiple IPs can be bound to the computer’s NIC, allowing for fine-grained control of bandwidth, traffic shapping, etc in their networking-hardware; each instance would then use the “Multi-IP” setting to only listen to specific IPs. (Management -> Settings -> Multi-IP)