Snodmaulvenn... The problems you have had with your Multiunit Flcs are basically incorrect indexing on the Unit Palette.
All simple to correct but I do not use GIMP. Blue Monkey uses GIMP and can help with that.
The Unit Palette Slots are indexed for the Slots that are used for specific things:
The Top Four Rows of 16 colors across each are for the "CIV Specific Colors" that change according to the CIV that owns the Unit.
The next 160 Colors are for the Unit Colors.
The Next 16 Shades are for the Translucent Smoke and Fog Shades.
The Last (Bottom Row) 15 Shades are for the Shadow Shades and the Transparent Background for Units.
The Palette is a 256 color Palette and because it starts with 0 the last color slot is #255 and that color slot is for the Transparent Background. #254 is the lightest Shadow Shade and generally not used with Unit Shadows but used for the Frame Lines on the Storyboard. Setting this Palette Slot as Green simply allows you to see the Frame Lines easier and also serves to block the Use of that Lightest Shadow Shade in a Unit.
It is Not the Color that makes something Transparent but the Color used on the specific Slot of the Palette. The Transparent color can be any color and the Game will use the Alpha.pal Palette, making that color Transparent due to the Palette Slot the Color is in.
The problem that has happened to Many people making Units is when they apply a palette to nearest Color Matching, All Graphics Programs will apply the first Color on the Palette that is closest to a Color. The "Smoke and Fog Shades" have extremely light Magenta Shades that are very close to Pure Magenta so a Light Smoke and Fog Shade is placed for the Background rather than the Magenta Color on Slot #255. You cannot see this Light Smoke Shade with the naked eye because it is so close to the Pure Magenta Color. In game, the Smoke and Fog Shade is seen as it really is... a translucent smoke/fog shade that is on the Palette.
The Palette we use is the .pal Palette. The Game uses the Alpha.pal Palette in the Game automatically. You can see this in Flicster by checking the Alpha Blend box.
When you apply a Unit Palette, check the Background to make sure it is the exact Color used on Palette slot #255 (Last Color on the Palette).
Most people Use Pure Green and Pure Magenta for #254 and #255 because those Colors are not usually used in Unit Images but the truth is you can use any color you like... just make sure the Colors you want to use are in the Correct Palette slots. #254 Palette Slot is the Lightest Smoke/Fog Shade is not generally used for Unit Shadows but is used when you have Smoke such as an Explosion or Gun Fire. Therefore, you can Block this Shade on the Palette by making it Pure Green for example if you do not want it used.
Not to confuse you but you can also use any of the same Colors that are visible in a Unit animation as Transparent colors because it is the index that sets a Color as Transparent not the Color... it is simply easier and also prevents index errors by using a totally different Color that is Not Used for any of the Unit Colors as the Transparent Color.
A Note about the "CIV Specific Color" Palette Slots:
As a General Rule, those Color Slots are all used for the Colors that Change for the CIV that owns the Unit. Just for your information, Not all of those Colors change.
I will post a Unit Palette with information and also a Unit Palette that shows the CIV Specific Colors that Change, Blocked out with Green and show the Colors that do not change.
The Blocked Out Smoke/Fog Shades (colored Pure Green) on the Unit.pal Palette Images are generally Not used but again this depends on what is wanted in the Animation.
If you use Civ3FlicEdit or Flicster, keep in mind about their specific problems (Post #27 above) so they don't cause you grief.