[MUMmer-help] MUMmer's issue with overlapping alignments (request for help)

[PLD <pla...@gm...>]

Dear all,
May I ask for your advice please?

At one point, when I was aligning a reference (NC_010079) to a set of
contigs, MUMmer recognizes two overlapping alignments:
1873926    1902489    65901    37311    28564    28591    99.90
2872915    65901    0.99    43.38    NC_010079    contig_64
1882538    1939799    57289    1    57262    57289    99.93    2872915
65901    1.99    86.93    NC_010079    contig_64

And consequently, dnadiff marks this as GAP:
contig_64    GAP    57290    37310    -19979    -19952    -27

As this is not what I expected, I tried checking the same region using
Blast.
I found that Blast saw this case as a single alignment (instead of two
overlapping ones):
contig_64    NC_010079    99.92    65902    26    16    1    65901
1939799    1873926    0    1.21E+05

Could this be one example of a known problem that you described on the
MUMmer 3 manual?
"nucmer, promer and run-mummer3 all have a difficult time with tandem
repeats. If the two sequences contain a different number of copies of the
same tandem repeat, these alignment routines will sometimes generate a
cluster on either side of the tandem and extend alignments past one
another, failing to join them into a single alignment region. This
generates two overlapping alignments and makes it difficult to determine
what caused this erratic behavior."
(http://newmbcrr.dfci.harvard.edu/mummer/index.html#nucmer)

If so, may I know if you have advice on fixing this please? Is there any
parameter that I can change to make MUMmer's results in this case resembles
Blast's results above?

I would really appreciate your help. Thank you very, very much for your
time!