Strandedness not behaving as expected

[cafelton]

I can't get intronProspector to output strandedness for every intron (required for FLAIR).

Here is the number of junctions I get with each strandedness option
default IP: {'-': 93148, '.': 742, '+': 99968}
IP w/ strandness RF: {'-': 93023, '.': 342, '+': 100493}
IP w/ strandness FR: {'-': 193321, '.': 342, '+': 195}

Attached is an image of a junction that resists being stranded, even though all reads aligning to it are on the positive strand.