RW 6.3.6 (15142) Publishing Issues

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RapidWeaver Version: 6.3.6 (15142)
System Version: 10.11.1
Hardware: MacBook Pro (Retina, 15-inch, Late 2013), 2.6 GHz Intel Core i7 Processor, 1 TB SSD Storage, 16 GB 1600 MHz DDR3 Memory.

Since this latest update, RW is selectively publishing my files even if I say all files and resources change before publishing. In one case, it actually removed the index.php and the other file I was publishing from my root directory and left my directory structure and all files exposed. When I discovered the files were missing I went to publish the files again and even though RW says it published, it never uploaded the main index.php file that was missing. I had to manually ftp it to the server.

I have been working with RW since version 3 and have never seen this behavior. FYI, exporting the files seems to work just fine.

Expected Result:
When I click publish on a single file, the file should upload and replace the file on the server whether or not I made a change to it. I am specifically telling it to upload and it should do it.

Additional Links:

Could you try Re-Publish All Files, from the File menu, and see if that corrects things?