I have run into the same issue. I had a program which would compile and run in R2013b but when I upgraded to R2015a and recompiled it I would see, "No class com.mathworks.toolbox.instrument.SerialComm can be located on the Java Class Path".
I fixed the problem by adding the following option to my call to mcc:
where [matlabroot] is the path returned when you run the command "matlabroot".
If you use the gui to compile I believe that you can get the same effect using the "File required for your application to run" section.