Completly refactored the way BungeeCord communication is handled. The code is now easy to update, test and maintain, and errors are more unlikely. This refactoring allowed to spot some issues that are now fixed.
Added Config: PlayerConnectionProcessingDelay setting in config.yml to allow to reduce the delay before processing a player connection, which can reduce the time when teleporting to a player/location on another Spigot server (thanks to DanRubMaster for reporting the issue).