It seems the software stops to work ad exit when number of R1 reads is greater then number of R2.
The error is because in fastq-lib.cpp qual.n returns -1 for the last record of the second file you pass :
if (fq->qual.n <= 0)
return 0;
and then with other reads it consequently fails.
But when R1 is lower, we still have -1, for reads 2, but the cycle stops and the error disappear.

When R1 reads is greater then number of R2, if you exchange the file in the command line, it works again.

If you have time...
Thank you.
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First of all, thank you for your work. I've found the "average join length" report somewhat misleading: one may think this is the average length of joined reads. Have you considered replacing this statistic with average joined sequence length?