I had the same problems (webhost being 1and1.com, I’m not surprised…) – I had to add the following two lines to my .htaccess file to force the use of php5. No idea why this was necessary but it fixed this problem entirely for me:
AddType x-mapp-php5 .php
AddHandler x-mapp-php5 .php
Hope this may help you.
Never mind, I fixed it myself… my files were getting corrupted here and there when I uploaded for some reason.
I fixed it myself, it turns out that about every 20th or so file I was uploading was getting corrupted… not sure why, but now all the files seem to be copying correctly. I wonder if my webhost was having issues the last few days or something.