Using Spigot with BungeeCord however neither are the cause of this problem as I have tested it with Vanilla too! This happens for all my players and depending on their hardware some have had their minecrafts brick for minutes at a time.
When the server tells the client to download a resource pack, the client can halt for a very long period of time. On slow computers the player will timeout and have their minecraft freeze for many minutes if they are on low-end hardware.
Here is a snippet from my log:
You can see that it took over 7 seconds to reload the resource pack. (This pack is empty and is used to clear the players resource pack but packs with content cause issues as well!)
Some of my players are reporting up to minutes at a time so please fix this.
EDIT: Critical info I noticed, if you connect with the direct IP address to the server there is no problem. If you use a domain name then it can take a very long time.