I couldn't figure out why this wouldn't work, a test script in the root of my htdocs folder worked fine.

Within some subdirectories the same code would produce different base64 results but I didn't know hwy.

Archive:  /tmp/archive.zip
Zip file size: 6888 bytes, number of entries: 92
error [/tmp/archive.zip]:  missing 242827681 bytes in zipfile
  (attempting to process anyway)
error [/tmp/archive.zip]:  attempt to seek before beginning of zipfile
  (please check that you have transferred or created the zipfile in the
  appropriate BINARY mode and that you have compiled UnZip properly)

Here was the problem in .htaccess!

It was because magic_quotes_gpc was being turned of by my htaccess within the subdirectory.

Now after disabling it the e-mail attachment zip is not corrupt and works fine but it was a big headache and definitely required a lot of digging/headscratching.

#php_flag magic_quotes_gpc off 
#php_flag magic_quotes_runtime on

*Update

It turns out that the real issue was just the "magic_quotes_runtime" being on.  It still works fine with the magic_quotes_gpc being turned off.