I just made the observation that omitting the DEFAULTS card does NOT default to the NEW-DEFA settings. I observed that the running time per particle (10 GeV proton) was much longer when I did not place a DEFAULTS card at all as compared to DEFAULTS: NEW-DEFA.
I compared the *.out files between the two runs, and I found that by omitting the DEAFULTS card the beam is set to a proton with a momentum of 200 GeV/c.
I did some tests and it looks like the problem is not the omission of the DEFAULTS card per se. (The NEW-DEFA options are still enabled, as far as I can tell)
The actual problem is, that the first card after an empty TITLE card is skipped. (If a GLOBAL card is present or the TITLE card is not empty, then there is no issue with reading the input.)