Ubuntu and Brother printing issues
I own Brother DCP-560CN printer. When printing on Ubuntu 12.10 (CUPS 1.6.1) I had two problems while using stock drivers from repository.
1. I could not print from apps that sends output as PDF (e.g. Libre Office - only in PDF mode, but when changed to PS file was printed) - in CUPS error log there were entries like
Send-Document client-error-document-format-not-supported: Unsupported document-format "application/pdf".
Then I realised there is no mime.convs file in /etc/cups - so I checked Internet and downloaded mime.convs file - problem was fixed.
2. Top margin was moved and page was cut. I found a solution on one of bug reports
brprintconf_dcp560cn -pt A4
(of course if you have different model you should change dcp560cn part to something relevant).
Now everything works fine.
Sad thing is that on Debian 6.0.4 (CUPS 1.4.4) everything worked out of the box when using drivers from Brother site (Brother driver on Ubuntu was producing same effects as stock one).
3 (bonus). If you are getting "No pages found!" errors while printing from Adobe Acrobat 9.5.4 (last version for Linux), deselect option in Print - Advanced - PostScript Options - Convert TrueType to Type 1. This option was removed in next versions of Acrobat.