I designed a multi-item sorter in in vanilla Minecraft, which works perfectly fine, however when I build it on a spigot server it breaks. The design is hopper minecart based and requires precise timings between the minecarts. On the server however a single minecart (very rarely) stop for a moment and then drive on, messing up those all important timings.

To recreate the issue I set up a spigot server on my laptop(from which I also play Minecraft) and build 3 things. 
1: a round track with powered rails with at leas 1 block space between both lanes. 2 powered rails going into opposite corners which can be powered at the same time such that 2 hopper minecarts can be put on the circular rail at the same time. 
2: a pen with about 800 chickens to stress my laptop such that the server can't keep up. 
3: some additional hopper minecarts on some other track.