Are all drives mounted as expected by the program?

I guess. I mounted my normal drive D (mount d d:\) were the game is on and E as my cdrom drive. (mount e e:\ -t cdrom)
So i have pretty much no clue what he wants.

I would recommend mounting D: as C and E: as D, as this is the way some DOS games expect it. Then, reinstall the game from the CD within DOSBox using those mount settings so it knows where to find the CD. Hopefully it should work.

didn't work. Does anybody has another idea?

Cannot open L:\xcom3\xcom3.cfd

Hmmm. It seems the program is looking for an L drive, for some reason. Try mounting CD-ROM drive as L: (just a shot in the dark).

Alright I found out that it obviously there is another problem:
Oh by the way it still doesn't work.
He tries to open ..xcom3\xcom3.cfg
Now here is the clue. The installed game on harddrive has a xcom3.cfg but no folder xcom3 und the cdrom has a folder xcom3 but no xcom3.cfg. Thats kinda wired.
Please stay with me on that.

I'd say you messed something with paths. You may need to reinstall it again. OR, do check your mounting commands. Check to see if game is seeing the paths as it should.

I reinstall it and again i hear the intro but do no see anything. At the end of the intro or if you cancel the intro by pressing a button it seems as it wanted to start the game it flickers and then you see the line:
C:\xcoma
thats all. i am going nuts here.