How does blastn sort output?
BLASTN should definitely report alignments in the order that the query sequences were provided.

Based on your description and my personal experience, I think the most likely explanation is some kind of mix up. It happens to all of us, especially when we're in a rush to get an answer, but even sometimes when we're being careful and disciplined.

If you can go back and recreate the result, I would be very interested to see the two pairs of input and output files. If not, I wouldn't spend too much more time worrying about it. :-)

UPDATE Alignments are reported in the order that the query sequences are provided, even in tabular mode. The order of each query's hits is sorted by bitscore or e-value, but that is a secondary sorting. I've included an example below that has two queries, seq1 and seq2 with -outfmt 6.

seq1    scaffold2       100.000 280     0       0       1       280     11131   11410   7.73e-146       518
seq1    scaffold294     88.693  283     25      4       1       279     12160   12439   6.46e-92        339
seq1    scaffold1525    85.315  286     29      9       1       277     27142   26861   3.07e-75        283
seq1    scaffold1874    83.505  291     32      10      1       280     8558    8273    1.86e-67        257
seq1    scaffold147     82.653  294     34      9       1       279     10797   10506   1.45e-63        244
seq1    scaffold2478    82.374  278     38      8       11      280     7622    7896    1.13e-59        231
seq1    scaffold3405    87.940  199     17      5       1       196     14390   14584   1.46e-58        228
seq1    scaffold395     83.060  183     23      4       106     280     12021   11839   5.40e-38        159
seq1    scaffold2853    85.965  114     13      3       1       113     20864   20753   9.16e-26        119
seq2    scaffold9       100.000 140     0       0       1       140     1121    1260    2.34e-68        259
seq2    scaffold2950    90.909  110     6       3       1       106     110     1       6.84e-34        145
seq2    scaffold3416    95.385  65      3       0       1       65      11882   11818   1.16e-21        104
seq2    scaffold3103    95.385  65      3       0       1       65      9736    9672    1.16e-21        104
seq2    scaffold5297    88.608  79      7       1       64      140     150     228     6.99e-19        95.3