First of all make sure you have the right I/O settings in Pro Tools in either cases, at home and at the Uniīs system.
Means, after opening Pro Tools always go to to the Playback Engine menu, make sure the Scarlett (or the Uniīs interface)
is selected, then go to the I/O menu and click on -Default- on every page (Input, Output, Bus, Insert) and press -OK-.
Donīt rely on itīs automatical re-routing, set it up manually to exclude any issues.
Secondly go to all your track channels and check the output settings, inclusive your busses and the Master channel. Make sure
they are all set up correctly accordingly to the I/O of the connected audio interface (Scarlett etc.). Check for any Mono settings
where originally there should be a Stereo setting for example etc.
Then donīt forget to save the session with all these settings.
You know, you always have to make sure that your channels meet the I/O settings of the connected interfaces, particularly if you
use different interfaces to work on your sessions.
You further may check out if you use the right version of OS X with your PT12.4
http://avid.force.com/pkb/articles/e...m-Requirements
and do set up all the optimization stuff as well as do some troubleshooting like trash Preferences etc. You can find it all there.
http://avid.force.com/pkb/articles/e...oting/en367983
To me personally it sounds like an I/O mismatch or there might be something set to Mono on your system or something like that.
Basically the Scarlett 2i2 works flawlessly with OS X El Capitan, Pro Tools 12.4 and 2014 MacBooks Pro and as long as the Focusrite
isnīt damaged there should be no reason why it should not work (no drivers and no software needed, just plug and play). Besides
my Apollo desktop system I use such a set up for mobile applications without any problems myself successfully.
Well, you additionally may check all connections (cables etc.) on your Scarlett set up, check your headphones etc. for possible
hardware failures.
All the best to you,
VRW