HDD Resetting after booting with SSD

I currently updated my 2011 Macbook Pro to include an SSD (sitting in the drive bay) with my HDD in the optical bay. All good—can easily switch booting between the two etc.

I'm using the SSD to run my Adobe CC applications. I had to install a 3rd party plug in for Indesign CC by booting into the SSD (where Indesign is installed).

However, upon booting back into my HDD, I had lost all my settings, such as which applications were on the dock, keyboard shortcuts, spaces and a whole bunch of other stuff. It seems as though it's taking on the settings of a fresh install?

So, why is this happening and how can I prevent it from happening in the future?

Thanks