First off, have you tried another PSX emulator to establish if this is a 'general' problem, or something specific with ePSXe?
Cause, to be honest, that is the only possible suggestion I can give to you. I don't think the File System of your hardrives is the culprit.
Just in the possibility that you missed this, make sure that in the memcard selection window, in ePSXe, each memcard is directed to the 'Saves' directory of ePSXe and that you've typed a name for each memcard i.e.
mempoopty.mcr
Let us know if the same thing occurs with other PSX emu's. You can give PSXeven, SSSPSX or PCSX a go. You can use the same plugins that you have with ePSXe.
r2rX
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