My failed installation didn't produce a .htaccess.rej file either. I have however successfully been able to apply the patch now. Note that disabling suhosin made no difference. The patch still failed with suhosin disabled in cpanles php version settings. Also note that I obtained the .htaccess file from the original zip file I still had for the 1.9.1 magento installation.
basically what I did was back up my existing .htccess file. I then ftp uploaded the original magento full installation zip into my existing shops top level directory where the problematic .htacess file lives. I then used cpanel file manager to decompress it which creates a new 'magento' directory that contains the fresh original .htaccess file in it. I then deleted the existing problematic .htaccess in the top level of my shop and copied the new .htaccess file from the new magento folder into my shops top level so I had the original version .htaccess there. I then ran the patch and it worked perfectly. I then deleted the zip and newly created 'magento' folder as no longer needed and job done.
You can then merge the backed up .htaccess with the new patched version, but in my case this wasn't necessary. The odd thing is prior to doing the above method, I decompressed the magento installation zip locally and compared the local .htaccess file with the live one and there was no discernible difference. So it would seem there is something indistinguishable introduced onto the .htaccess when it is decompressed locally that caused the patch to fail in a live setting. Decompressing the zip on the live sever instead and moving files around in that environment using either shell or cpanel file manager seemed to resolve this problem.
It's worth noting though that 6788 makes enough significant changes to your magento installation that I'd strongly recommend testing it first in a test environment to ensure it doesn't break any part of your shop as there are a number of aspects that could do this. It is by no means as 'easy going' on your shop as the prior patches so take necessary precautions and full backups and do some testing prior to patching.
@robbyotts
I think the reason the .htaccess.rej file may not be produced is there is nothing to put in it. As mentioned there was no discernible difference in my .htaccess files prior to patching when comparing them both on my local drive, however the patch obviously sees something minuscule causing the error. You could perhaps compare your 2 htaccess files yourself prior to running the patch (as in the current one in your shop and the original one that the decompressed zip produces) to see if it's the same for you as well since we both experienced the same error. If they are indeed the same it may be that there will be noting to merge and once the patch is run and you won't need to do anything further with your new patched htaccess file.
