Ok it turns out that the EX4600's do eventually take on the role of master and backup and all interfaces then come back up.
However, this takes about 15 min! If I plug the EX4300 in, it happens within a minute or so.
Why does this take so long for the 2 EX4600's to work out the master/backup role when the EX4300 is not connected? Can this be sped up?
To answer the questions: THese switches are interconnected via 40gb vcp ports, single links. no-split-detection is not currently configured, however it was initially present during the first powerup without the EX4300, because I had initially configured no split detect when first setting up the VC (just had the 2 EX4600;s). The issue is present with or without the no split option.