Thank you Torsten and Greg.
When I reopen the .nrrd file with Fiji and check the properties I have this :

NRRD0004
# Created by Nrrd_Writer at Wed Mar 23 16:50:58 CET 2011
type: uint16
encoding: raw
endian: big
dimension: 3
sizes: 1024 640 119
space dimension: 3
space directions: (0.013888888888888888,0,0) (0,0.013888888888888888,0) (0,0,1.0)
space units: "cm" "cm" "cm"
------------------------
Title: flt.nrrd
Width: 14.22 cm (1024)
Height: 8.89 cm (640)
Depth: 119.00 cm (119)
Resolution: 72 pixels per cm
Voxel size: 0.01x0.01x1 cm
ID: -2
Coordinate origin: 0,0,0
Bits per pixel: 16 (unsigned)
Display range: 88 - 467
Image: 1/119
No Threshold
Uncalibrated
Path: P:\FirstConfoca1403l\flt.nrrd
No Selection

So I don't know exactly what you meant with "sensible properties" (voxel size), but it seems to be defined.
Using the command with -v like Torsten proposed, I have roughly :

... ref.nrrd
Read 1024x512x102 voxels [14.208333 x 7.091222 x 101.0000 mm total size].
Date type ushort <16bit unsigne>, range [61 .. 4095]
WARNING: image does not have valid orientation meta information;cannot reorient.
Read 1024x640x119 voxels [14.208333 x 8.875 x 118.0000 mm total size].
Date type ushort <16bit unsigne>, range [83 .. 4095]
WARNING: image does not have valid orientation meta information;cannot reorient.
Entering resolution level 1 out of 5...
Entering resolution level 1 out of 5...
Entering resolution level 2 out of 5...
Entering resolution level 2 out of 5...
Entering resolution level 3 out of 5...
Entering resolution level 3 out of 5...
Entering resolution level 4 out of 5...
Entering resolution level 4 out of 5...
Entering resolution level 5 out of 5...
Entering resolution level 5 out of 5...
Resulting transformation parameters:
#0: 0.0
#1: -0.88889
#2: -8.5
#3:-0
#4:-0
#5:-0
#6:1.0
#7:1.0
#8:.10
#9:0.0
#10:0.0
#11:0.0
#12:7.104
#13:4.4375
#14: 59
#

And I have no affine.xform file or directory anywhere. (it should be in the same directory as where registration.exe is or in the directory of my images ? I also tried
and nothing appears)

(By the way, I struggle to have this output automatically in an output file of in my clipboard and it does not work, using different windows command :
I also noticed that after one or two computations (I run it first, then a bit later the same task) the program crashes : windows says "registration.exe has stopped working" and in the command line I have

... ref.nrrd

Read 1024x512x102 voxels [14.208333 x 7.091222 x 101.0000 mm total size].

Date type ushort <16bit unsigne>, range [61 .. 4095]

WARNING: image does not have valid orientation meta information;cannot reorient.Read 1024x640x119 voxels [14.208333 x 8.875 x 118.0000 mm total size].


Date type ushort <16bit unsigne>, range [83 .. 4095]


WARNING: image does not have valid orientation meta information;cannot reorient.

Entering resolution level 1 out of 5...
Multi-level R

For my next scans, I´ll use the format directly given by my microscope (olympus > oib), and see what it gives.

Greg, I'll take a closer look at what you have done for fly brains registration, that's what I would like to do.#

Thank you for your help

Thomas