What is splice junction pairs?
Splice junctions are the exon-intron junctions, at which splicing takes place. 
Splice junction pairs are the pairs of such junction (to cut an intron you need to splice in two junctions).
So, you are almost there, since two exons will be joined in correspondence of two subsequent splice junctions.
You might find these slides useful (slide B-6)



EDIT:

As Adam pointed out the slides are no longer available. I have no idea on where they are gone, but I suggest referring to the following wikipedia pages for an introduction:

RNA splicing

Exon junctions

Alternative Splicing