Hi @peter,
I haven’t actually tried to generate a multiple files per subject scenario for the GUI job generator. I’ll take a look at this when I have time.
In the mean time, you could try setting the jobfile up as .m file. There is an example in the .../osprey/exampledata/sdat/MEGA/jobSDAT_MEGA_Multidataset.m file and also some more discussion here (4 MRS acquisitions per session in IMA format - #3 by Remy).
Let me know if this works for you.
Best,
Helge