Cheers for the suggestion djaydino, I've attached an image of the animator and the FSM to help illustrate the issue.
In the image of the animator I've highlighted the transition that is named "Scan to Scan Shutdown".
The part that baffles me is that it works on the first time round but not any time after that.
As you can see "Scan Off" is the entry state where it stays idle until a different FSM (not pictured here) sets the animation trigger "Scan_Activation", then the animation "Scan Startup" plays and then "Scan" loops until the FSM (the one not shown in the images) sets another animation trigger "Scan_Deactivation" which begins the transition "Scan to Scan Shutdown" then the animation "Scan Shutdown" follows and once complete it returns to the "Scan Off" animation.
As I say this works perfectly on the first cycle, then on the second loop it syncs everything but the "Scan to Scan Shutdown" transition.
Is this normal behavior, that it only works on a single cycle through the animations or have I miss-used it?
And in answer to your question yes with only 4 states it does work as you'd expect, however I have an animation on another object that relies on knowing when the transition begins rather that when the next animation finally begins. Regardless of that though each state currently gives a valuable instruction to elements of the game, so I'd struggle without the transition sync state.