usage of make -j# may not be related (but another issue - covered by problems
with gmo builds).

If I run:
make
make clean
make

there will be differences in the files mentioned above.
build output:
----------
Making all in graphics/floor_tiles
make[2]: Entering directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/graphics/floor_tiles'
make --directory=../../gluem/
make[3]: Entering directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/gluem'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/me/localbuild/SRCs/freedroid/freedroid-code/gluem'
./../../gluem/make_atlas floor_tiles_atlas 2048 1024 atlas.txt iso_*.png */iso_*.png
Creating atlas in atlas.txt from 257 images.
Atlas 1 created. Last y position is 1022. Atlas size: 8192kB, images size:
7706kB. Packing efficiency is 0.940716.
Atlas 2 created. Last y position is 202. Atlas size: 2048kB, images size:
1187kB. Packing efficiency is 0.579704.
make[2]: Leaving directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/graphics/floor_tiles'
Making all in graphics/obstacles
make[2]: Entering directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/graphics/obstacles'
make --directory=../../gluem/
make[3]: Entering directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/gluem'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/me/localbuild/SRCs/freedroid/freedroid-code/gluem'
./../../gluem/make_atlas obstacles_atlas 2048 2048 atlas.txt iso_*.png */iso_*.png
Creating atlas in atlas.txt from 518 images.
Atlas 1 created. Last y position is 2047. Atlas size: 16384kB, images size:
15352kB. Packing efficiency is 0.937025.
Atlas 2 created. Last y position is 2047. Atlas size: 16384kB, images size:
15714kB. Packing efficiency is 0.959107.
Atlas 3 created. Last y position is 356. Atlas size: 4096kB, images size:
2397kB. Packing efficiency is 0.585208.
make --directory=../../gluem/
make[3]: Entering directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/gluem'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/me/localbuild/SRCs/freedroid/freedroid-code/gluem'
./../../gluem/make_atlas obstacles_shadows_atlas 2048 2048 shadow_atlas.txt
shadow_*.png # */shadow_*.png
Creating atlas in shadow_atlas.txt from 172 images.
Atlas 1 created. Last y position is 1121. Atlas size: 16384kB, images size:
8174kB. Packing efficiency is 0.498962.
make[2]: Leaving directory
'/home/me/localbuild/SRCs/freedroid/freedroid-code/graphics/obstacles'
----------
again - this is "repeatable"