The problem is that the TIFF fileset does not contain adequate projection information for the TIFF, so you have to enter that manually. Enter it manually and it works perfectly.
This bit is misleading, by the way, in that it sends debugging off in the wrong direction:
I'm experiencing some issues when importing tiff images into M9. In M8 this process always worked and still works fine, but when importing the same image file (tiff) into M9 the projection is always off with all images appearing at the same place.
As it stands, the above makes it sound like the TIFF imports into 8 correctly, but not into 9. That is incorrect. It appears it would have been better to say "this TIFF doesn't import correctly into either 8 or 9, but I've come up with a procedure to get it georegistered into 8. Here it is step by step [...]. What would be the equivalent procedure in 9?"
The TIFF does *not* contain projection information that either Release 8 or Release 9 can use. It does not import into 8 correctly and it doesn't import into 9 correctly. It also doesn't import using GDAL correctly.
The procedure given for a successful import into 8 seems to be not possible as written...
Edit > Assign Projection > SGHM (Sistema Militar, Datum Lisboa)
... as there seems to be no SGHM (Sistema Militar, Datum Lisboa) choice in the Release 8 Assign Projection dialog. So... what did you do in Release 8? If there is a SGHM choice in a Release 8 dialog, how do you get that dialog?
In the Release 8 map you provided (good move), the TIFF image uses a Transverse Mercator projection centered on a given lat/lon with a WGS84 datum with false easting/northing offsets and custom local scale and custom local offset. If you use the same settings in 9, that also works in 9.
In 9, get rid of the useless TFW and import the TIFF and choose Assign Initial Coordinate System, then specify a custom coordinate system using exactly the same parameters as used in 8. However, instead of using the WGS84 datum (referred to as the "Base") use the Lisbon EPSG:4207 datum. That's what the meta data says the coordinate system uses, so specifying a different datum could introduce significant errors.
Do that, and the image lines up perfectly (compare roads, waterways and railways), as compared to a background layer of Bing Streets:
In the image above you can see the military map does not include the A23 highway, the broad purple line toward the right of the map. Perhaps the military map was created before the A23 highway was built. Or, maybe in an austerity campaign they don't want to pay tolls to use the A23, if it is a toll road. (Just kidding :-).
I suggest a careful re-reading of all topics having to do with assigning projections/coordinate systems in 9, so you know how to assign local scale and local offsets, as well as the difference between a datum and a projection.
This, for example, is a mistake as a procedure in 9:
Repair Initial Coordinate System > Datum Lisboa IGP (System similar to Datum Lisboa)
The Lisboa datum is a datum, a base, not a coordinate system. You have to specify a coordinate system.