I found a workaround:
1. Click on your Home planet
2. Click on the "Rename" button
3. Click on the "Done" button
4. Send your colony ship to the planet and colonize
5. Type in your planet name (while typing in you will not(!) see the name. it will be left blank. )
6. Click on the "Done" button
Now you can see the name on the map.
I hope this problem will be patched away. Are you working on this?
I found something interesting concerning my problem: http://forums.galciv2.com/105780
Maybe it is related to it?