Update
Thank you Ildar for being so responsive and looking into everything. Everything on the x-cart side looks good and my patch.log shows everything patched correctly. And since nobody else has reported any issues it must be an isolated incident with my files.
My first thought while doing the file comparison was that I screwed up and uploaded a 4.6.4 backup instead of just the (5) manually patched files. But, 3 things tell me that this is not the case. First, my ftp program would have been uploading files for quite a while and I would have been just sitting there watching the files upload. Second, I checked some of the files that did not need editing and some of them were 4.6.5 version files. And third, I only had to patch 30 to 40 files and not the full 189 in my file.lst.
I do think it is good practice after upgrading to use a file comparison program like Beyond Compare to quickly check your upgraded files against a full version download to make sure the only differences are manual edits.
Thanks again!
Paul