Interesting issue. Do you see this problem also elsewhere (e.g. on the same machine where you run FTP Voyager) or is it only on this combination of machines? What is the FTP server version? Have you been able to simulate situation in which remote files are newer?
Peter I have replied to you in email and had no response. In case you didn't get it this is what I sent:
I reported this bug in the Thwack forum back in October and have had no response. We originally purchased this product and have upgraded to the latest version to resolve other issues in the past. After several prompting via Facebook I noticed you have posted a response.
Our setup has been to use FTP Voyager Scheduler to periodically perform our synchronisation task. We constantly update our local folder by adding, updating and deleting files. Our remote machine needs to reflect the same with its folder. The remote machine only enquires the files it receives. It does not perform any changes to the content of the synchronised folder.
The problem I’m reporting was only discovered when updates were not being synchronised to the remote site because of the Ignore Older setting. When that was turned off the synchronising task began to take longer to run. The reason for this apparently the transferred files were still considered out of date hence the repetitious synchronisation. We have over 10,000 files in our sync folder and do not to upload all of these every time.
I ran a simple test just by using the FTP Voyager app and manually performed a sync and as you can see from the print screen I posted on the forum the results show the date and time are identical yet FTP Voyager still considers the folder out of sync.
According to the log we are connecting to Microsoft FTP Service. Since FTP Server runs within svchost.exe I checked the version of C:\Windows\System32\inetsrv\ftpsvc.dll on the remote machine and its 7.5.7601.17855.
From the log I noticed after the HOST command it returns 504 Server cannot accept argument. Not sure if that’s an issue.
Further down it reads
 Fri 11Dec15 00:00:01 - SYST
 Fri 11Dec15 00:00:01 - 215 Windows_NT
 Fri 11Dec15 00:00:01 - FEAT
 Fri 11Dec15 00:00:01 - 211-Extended features supported:
 Fri 11Dec15 00:00:01 - LANG EN*
 Fri 11Dec15 00:00:01 - UTF8
 Fri 11Dec15 00:00:01 - AUTH TLS;TLS-C;SSL;TLS-P;
 Fri 11Dec15 00:00:01 - PBSZ
 Fri 11Dec15 00:00:01 - PROT C;P;
 Fri 11Dec15 00:00:01 - CCC
 Fri 11Dec15 00:00:01 - HOST
 Fri 11Dec15 00:00:01 - SIZE
 Fri 11Dec15 00:00:01 - MDTM
 Fri 11Dec15 00:00:01 - REST STREAM
 Fri 11Dec15 00:00:01 - 211 END
 Fri 11Dec15 00:00:01 - Server supports resume.
 Fri 11Dec15 00:00:01 - OPTS UTF8 ON
 Fri 11Dec15 00:00:01 - 200 OPTS UTF8 command successful - UTF8 encoding now ON.
 Fri 11Dec15 00:00:01 - File dates and times will be automatically adjusted for the local time zone by 600 minutes.
What I’d like to know is have you been able to reproduce this issue?
Let's take this offline this seems like a complicated issue which may be easier to discuss directly. I'll continue in our email thread.
Peter can we have an update on this. I have tried corresponding with you offline but have had no replies.