If I understand you correctly,
3 fifo's working great on 3 different plc's
you have a conveyor system (for example) which is fed by these 3 plc systems.
they all merge onto the last conveyor at the same point.
if this is the case, may I suggest the following.
1. allow 2 of these conveyors to merge together and create a fifo for them.
then merge this line with the last conveyor and create a final fifo.
OR
2. create staging logic for the 3 systems to merge into the last system.
this will involve a fifo for the staging of the containers.
since I don't know your exact layout, I can't give much help beyond this.
I used to work for a conveyor oem and we had to stage things, they just couldn't all hit the last conveyor at the same time for the reason you are experiencing, 2 or more boxes entering at the same time. the fifo got confused.
james