I think it's rather important to note that the current Vasari have had no direct contact with the mysterious foe - they have only seen the crew of the one ship that returned from the battle, driven insane, and based on that decided to flee.  So, they likely have no idea that the phase jump inhibitor is the (likely) cause of their plight, and have probably still been leaving them behind all throughout their exodus.  This makes them the perfect way to track the Vasari, if they are indeed some sort of beacon.  That the other races are now stealing and redeploying them worsens this danger, and I'm interested to see where the plot goes with regards to this.

Nanites could be a possiblity. Maybe during the experiment of transporting nanites through phase space they became self aware and turned on their creators. The nanites are drawn to the energy of the PJI and use those to track the vasari and to destroy their creators.

This is getting far too specific for the information we have.  Speculation is fine, but not to the point where it no longer follows in any obvious way from the lore.

Since the Steam achievement says something about ponies, I have been thinking some kind of insufferable, effete, cartoonish ponies were chasing them.  But your notion sounds cooler by far.

My bugs will eat their ponies.

Volt, that is an awesome rendering.

They said it was in the game code... so its in the game code -__- it was something for modders to find.

Also this WAS for modder's to find and in a sense it is a code, just not the computer language type. 

Regarding speculation on what has the Vasari running, just my theory.

Perhaps the beginnings of it are already here. Perhaps the salvers are slaves themselves. The Loyalist are already defeated and the Rebels are the only hope to save their kind. The Vasari home systems are completely destroyed and now there is nothing but machines and they are expanding, at the moment unstoppable.

http://www.youtube.com/watch?v=90D44l8qiBM

The actual quote:

"It's my personal mission to encode some top-secret stuff into the code that's going to give you some really good hints about what's going on...and I know the modders are really smart and they always go through all our data files to try and reverse engineer and find out what everything is, so I'm not putting it in there.  I'm gonna actually encrypt it into the code so that they don't just find it right away and reveal it to everyone else."

They said they encrypted it somewhere where modders wouldn't instantly find it. So..

Not sure where that would be as im not a modder, but its definitely not in your normal area.

Just a thought. Perhaps if its encrypted in the code, maybe its like the textures of the Vasari Corvettes, in that you need to put code from one thing together with code of another.