So when you got the "Lost connection" error, you did not allow WinSCP to reconnect and continue, correct?

Anyway, I do not think that FileZilla does not have the problem.

There's about 10 reconnects like:

2016-05-25 14:28:28 5820 3 Opdracht: PASV
2016-05-25 14:28:28 5820 3 Fout: Verbinding gesloten door server
2016-05-25 14:28:28 5820 3 Fout: Bestandsoverdracht mislukt
2016-05-25 14:28:28 5820 3 Status: Verbinding met server verbroken
2016-05-25 14:28:28 5820 3 Status: Adres bepalen van xxxx
2016-05-25 14:28:28 5820 3 Status: Verbinden met xxxx:21...
2016-05-25 14:28:28 5820 3 Status: Verbinding aangemaakt, welkomstbericht afwachten...
2016-05-25 14:28:28 5820 3 Antwoord: 220---------- Welcome to Pure-FTPd [privsep] [TLS] ----------
2016-05-25 14:28:28 5820 3 Antwoord: 220-You are user number 3 of 200 allowed.
2016-05-25 14:28:28 5820 3 Antwoord: 220-Local time is now 14:28. Server port: 21.
2016-05-25 14:28:28 5820 3 Antwoord: 220-This is a private system - No anonymous login
2016-05-25 14:28:28 5820 3 Antwoord: 220-IPv6 connections are also welcome on this server.
2016-05-25 14:28:28 5820 3 Antwoord: 220 You will be disconnected after 30 minutes of inactivity.
2016-05-25 14:28:28 5820 3 Opdracht: AUTH TLS

The difference is that FileZilla reconnects silently, while WinSCP displays error message and reconnects only after 30 seconds (by default).

Log files attached.

<logs deleted by admin 2x>

I have sent you an email with a debug version of WinSCP to the address you have used to register on this forum.

Can you also post a logs from the "alternative clients"?

It happends after approx. 1 minute of transfer. I always use Wordpress zip to test and it happends like 4 times. Not always the same. (talking about uploading right now).
It's only for one specific server, thats weird, but there are no misconfigurations or other problems at the server. Several alternative FTP clients have zero problems.

Thanks.

(Maybe I can provide you with an account to test with if you want).

Thanks for your report.

How often does it happen? = How easy/difficult is to reproduce the problem?

I got timeouts after some time when uploading or deleting lots of files (for example wordpress installation).

Log of WinSCP attached (some parts removed due to it's sensitivity or repeating factor).
Server is PureFTPD. Firewall is not the issue (at server side), (tried without it too).

Server log doesn't give weird entries, 'just' a disconnect somehow.