Quit being stubborn, 90% of the community experience connection lag at least half of the time they connect to siege.
It has been lagging ever since you installed bungeecord. That shitty plugin has a fucking bad way of dealing with world loading, makes your server use an incredibly high amount of RAM, makes spigot crash for no reason, has a shitty "garbage collection" method that makes you need to reboot the server every week minimum, and has only one freaking advantage : the /server command. Oh, sorry, the /glist command too. Forgot that one.
I really REALLY don't mind having the /server command removed if it's to kill that lagging.
Also, bringing back craftbukkit will fix most of the bugs you experienced lately. Spigot is "good" if you really don't know how to manage a server's performances. It's really bad for big servers.
Now, to explain my first post : when logging in, if you experienced the long "downloading terrain" screen, all your gaming session would be laggy. If you didn't see that screen for so long, it wouldn't be. Now, that issue has moved to something even more annoying : the loading screen doesn't pop up anymore. The world just doesn't load, because spigot/bungee (dunno which one of them does that) throttles the downloading speed for every session, and diminishes the view distance per-player. It works good when there are a GREAT maximum of 20-25 players online, but starts to work like shit when there are more. You always login when there are 20 or less people. As of lately at least. And you can't see that problem for whatever reason, mainly because you're in the netherlands and you have a good proximity between you and the server. But for everyone who has to use the Amsterdam internet exchange point (meaning all the countries in the world except nordic countries, the baltics part of russia), it's slow as hell. Because Amsterdam's IEP has a "tiny but noticeable" lag that makes Spigot/Bungee think that our connection is shit. Meaning spigot/bungee throttles the session of all the players because it guessed something wrong.
Also, I'm fairly certain that the anti-ddos (if still present) plays a good role there. Disabling it would be a good thing imo.
Last but not least, this whole thread applies to the "huge" connection lags, those who have more than 5 seconds delay. Less than that is standard intercontinental/international lag and is fairly normal. And yes, those huge connections lags happen. I'm often able to fly on the whole Tirith map (at least in the loaded chunks) for 2 freaking minutes before being knocked back to my initial position. Or receiving a "you died" message because someone hit me 2 minutes ago.
The only thing you can do here is disable bungee and go back to craftbukkit. Spigot is useless if you don't use bungee or don't absolutely need its anti-xray. Plus it creates some incompatibilites with your plugin.