Hi, you're correct that C1_C2 and C2_C1 both refer to the exact same junction coordinate (exon skipping). However, from MAJIQ's point of view, this junction is quantified twice: once from the point of view of exon 4 and once from the point of view of exon 6. Although the numerator is the same from both points of view (MAJIQ utilizes the same split reads when quantifying this junction), the denominator can (usually does) differ from exon 4 vs exon 6's point of view.
Exon 4 is the reference exon for a source LSV (hence the "s" in the LSV ID), and MAJIQ quantifies splicing for the LSV from exon 4's point of view: which junctions start from exon 4? C1_C2 and C1_A.
Exon 6 is the reference exon for a target LSV (hence the "t" in the LSV ID), and MAJIQ quantifies splicing for the LSV from exon 6's point of view: which junctions end in exon 6? C1_C2 and C2_A.
In a perfect world, with perfect RNA-Seq read coverage, a simple cassette exon would have equal numbers of reads for C1_A and C2_A. However, technical (and biological) variations often cause differences in read coverage between C1_A and C2_A (in the cartoon, you see that there is 10 vs 17 reads for eg). Also, if the module is complex, there may be other junctions that splice from exon 4 or into exon 6, which would further cause differences in the source vs target LSV quantifications of the exon skipping junction.
-Caleb Radens