Filtering bam file with bedtools intersect using strand specificity
Your bed file switch the score and strand columns. Strand should be column 6, score column 5. For example take this bed file with the 5th and 6th columns switched - zero results for strand specific intersection b/c strand is actually '.'

$ cat wrong.bed
chr1    30000000        31000000        noname  +       .
$ bedtools intersect -a mm10_500k_pe.bam -b wrong.bed -wa -u -f 1.0 \
    | samtools view | wc -l
166
$ bedtools intersect -a mm10_500k_pe.bam -b wrong.bed -wa -u -f 1.0 -s \
   | samtools view | wc -l                              
0


After fixing the bed file:

$ cat right.bed
chr1    30000000        31000000        noname  .       +
$ bedtools intersect -a mm10_500k_pe.bam -b right.bed -wa -u -f 1.0 \
      | samtools view | wc -l
166
$ bedtools intersect -a mm10_500k_pe.bam -b right.bed -wa -u -f 1.0 -s \
      | samtools view | wc -l
83