The maximum length of an input filename in all AFNI programs is 256 characters. Your input is 369 characters long (after the awk expansion). I suspect that this is the problem.
Without recompiling the programs, you could try splitting your 1D file into 2 files, so that there are fewer "1" values in each file, as in taking
{0 1 1 0 1 0 1} into
{0 1 1 0 0 0 0} and
{0 0 0 0 1 0 1}. Then use 2 awk inputs one the command line, as in
3dTcat scaled_RMTB+orig\[`awk '/1/ {printf "%d,", NR-1}' a.1D`\] scaled_RMTB+orig\[`awk '/1/ {printf "%d,", NR-1}' b.1D`\]
where a.1D and b.1D are the two 1D files that together specify the desired sub-bricks.
