To be clear, even if you've disabled (or not even configured) virtual-chassis in your config, ports will remain virtual chassis uplinks if configured that way. If you've confirmed with the show vc-ports command that they are not vc-ports then I would delete the two et interfaces on both ends and configure as below as a quick test, adding the no-autonegotiation only to the EX4300. There is a autonegotiation bug in at least one of the 14.1X53 versions when connecting to qfx/ex4600, it may also be in 13.x.
EX4300:
et-0/1/x {
ether-options {
no-auto-negotiation;
}
unit 0 {
family ethernet-switching;
}
}EX4600:
et-0/0/24 {
unit 0 {
family ethernet-switching;
}
}