The difference between these fcs files are the following:

Regular FCS 3.1 specification:
EY_2013-07-19_PBS_FCS_3.1_Well_A1.001.fcs

FCS 3.1 custom with additional information:
EY_2013-07-19_PBS_FCS_3.1_Custom_Add_Well_A1.001.fcs

FCS 3.0 custom without additional information (probably same as regular):
EY_2013-07-19_PBS_FCS_3.1_Custom_Without_Add_Well_A1.001.fcs
