I ended up running my input file from the command line last night via /usr/local/fluka/bin/rfluka -M 1 -d BB5_Si_Al.inp, forcing it to use flukadpm with the -d flag. Success:
If you launch the simulation from Flair, you have to select the executable in the Exe field of the Run tab.
Thanks for pointing that out. I will use that in the future.