Hello Martin,
Taking your submitted Nominal.inp and replacing 50 by 500 in the Max1 field of USRYIELD I do not reproduce your crash. There is however something weird in your output messages: 98 (as you see in your Nominal_98.yie error message) is the unit number for your commented (inactive) USRBIN; the USRYIELD output is written instead to unit 30. So at some point in your attempts something got corrupted. Go to the Data tab, refresh and scan. If all fails, start afresh: flair Nominal.inp
The default binary you get with your FLUKA installation contains the nucleus-nucleus event generator for energies of up to 125 MeV per nucleon. If at some point you need to run a simulation transporting heavy ions at higher energies (like in your accidental case above) the default binary does not suffice: one has to link a new binary including the nucleus-nucleus event generators at higher energies. This can be done either in the terminal with “ldpmqmd” or via Flair (Compile tab -> select ldpmqmd instead of lfluka -> click Build and then in the run tab -> Runs you should load the resulting binary in the “Exe:” field). I had the suspicion you ran without, so I tried without: since the random-number seeds written to my.err matched with your Nominal001.err this was sufficient proof that this was the case, so I raised alarm 
Cesc