I had this issue as well using the reference files that came with the tool, and it turned out I had a 1-off error- on the Start_position in the input mutation file. It should be 1-based relative to the Reference_Allele.
The way I figured this out was to check the base at specific positions in the provided reference files with commands such as head -c <position> chr1.txt|tail -c 1 and make sure the output matched the Reference_Allele base(s) in my input maf.
If you wanted to use a custom genome build instead of the hg19 provided, your format would probably need to be similar to the provided files, 1 file per chromosome with no linebreaks, so you'd have to convert a typical fasta accordingly (something like cat <your_reference_fasta_chromosome>|grep -v ">"|awk '{printf $1}' > <out_chr.txt>