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I am trying to figure out what change a new admin made to cause this to happen. I had a test company setup for GP 2015, everything worked great but now due to some change made (I'm thinking in Smartlist Builder) every time a change to a smartlist is made the Test company it also changes in the Live company. It appears that changes to the users "profile" in GP also changes (i.e. if I add buttons to the menu in one company it does the same in the other). I'm pointing towards something changing in Smartlist builder because I see a lot of new reports he created in there and that is when the issues started happening.
Have you checked with newly appointed GP admin that he/she does not create new multi-company smartlists ? Under SmartList Builder > Options > Summary you have the option of making any SmartList (or Excel Report) multi-company aware, which would eventually result in what you experience..
I'd also try to post your question on the SmartList builder Forum on eOne's web site.. there might be a chance some support engineer from eOne would have a more suitable answer..