The PHP Generator adds trailing whitespace (2 newlines it appears) at the end of each file.
This became a problem for me when I included the generated file in a script which outputs an image. The 2 newlines corrupted the image data which followed.
Apparently CVS needs a blank line at the end of files, so if this is the reason for the superfluous newlines, perhaps a better idea would be to...
2009-03-23 06:13:21 UTC in Druid, The Database Manager