I, too, experienced the same problems despite changing the appropriate settings in Preferences for MATLAB R2018a on Ubuntu 18.04. The problem was fixed for me by using the -useStartupFolderPref flag as mentioned above. For future reference, my working Ubuntu .desktop launcher file now reads:
Exec=matlab -desktop -useStartupFolderPref
StartupWMClass=MATLAB R2018a - academic use
The "StartupWMClass" line fixes the potential presence of many instances of MATLAB open in the dock.