When the Minecraft server pushes up to the client a Resource Pack to use, the client is setting the name of the RP to "Server" instead of the filename when the player adds a RP themselves to the same list. The problem is two fold.
1. If multiple resource packs are sent to the client, only the last one would remain which I assume has to do with the naming convention used when receiving a resource pack from a server. The name should not be "Server" - it should be the filename or Server-1 or Server-A or a unique name keeping it distinct from other RPs sent up. Players should be allowed to have/use more than one Resource Pack as that has been supported for a number of releases.

2. The player can only have one named plugin since it wouldn't allow a duplicate and additional RPs sent to the client replace the previous one that is named "Server". <--this is an assumption given the behavior of not being able to use more than one stacked RP for the player. If we must keep it as "Server", the code should validate which plugins have been pushed up and stack it properly. See screen shot.

I've already asked Spigot & the Plugin owner and both state there is no exposed API for them to call and change the name of the RP being sent. They only call the existing hook in the client to upload/apply the RP. Both resources state this is a Mojang bug/enhancement to handle. Thanks for your time and consideration of this. -Steve