Ok I now got the problem right:

XD1v0 is correct about the alpha blending error, that's what I saw as visibility problem. However there is one thing left.
I used several .png images and none of them contained an alpha channel!

It is possible for both the .png and the .tga format to have an image saved with or without alpha channel applied. This can be controled using the channel dock in e.g. gimp.
When loading a .tga file without alpha channel into med, the skin is proceeded in the right way and created as 24bit without alpha. However when loading a .png file into med, it seems that automatically a pure white alpha channel is created.
The texture format is set to 32bit with alpha, althoughh there is no alpha channel in the image.

Of course it's not that great problem to deactivate the alpha channel for each .png texture, but it would still be good, if you could change that behaviour, if possible.