MACS was developed in the days of short single-end reads. As far as I know, it can autodetect the file type (SAM, BAM, BED, Eland...), but you have to indicate if paired-end reads are present of not. I would write your SAM files as BAM (
samtools view -b in.sam -o out.bam), and then add to your command
-f BAMPE. You can also check from the stuff MACS writes to
STDERR if MACS says "read treatment tags" (indicating single end) or "read treatment fragments" (indicating paired-reads, because two reads are read that are sequenced from one fragment).