Jon,
The FTP
Do you have FTP commands logging turned on? (FTP_COMMANDS_AND_RESPONSES_LOGGING ON) If not, you'll need to turn logging on. The way you do this is to create a plain text file named PMDebug.txt in your Photo Mechanic Preferences folder. The file simply needs to contain the following:
FTP_COMMANDS_AND_RESPONSES_LOGGING ON
Your PM preferences folder is located in the following location:
<your home folder>/Library/Preferences/com.camerabits.PhotoMechanic/ Unfortunately, Apple decided to hide the Library folder by default. You can get around this by using the "Go to Folder" command on the Go menu in the Finder and entering: ~/Library/Preferences and then confirming the dialog.
If the PMDebug.txt file is found in your PM preferences folder then any settings turned on will be used by PM. If you then try your upload, your PM.log will then contain a transcript of what commands were sent to and responses received from your FTP server. It may be that your server doesn't allow a file to be replaced. Seeing the log will help us determine this.
Once you've tried uploading the same file an additional time, go to the Help menu and choose "Reveal Support Data..." and moments later a Finder window will come forward with the zipped log file selected. Use the 'Attachments and other options' link when you're composing your reply to this message and there you'll be able to upload your zipped PM log file.
Thanks,
-Kirk