Fixed in 5.2.2 beta and released today.

Ok, I see. You are right, it's not working correctly. Thanks for being persistent!

This bug has been added to the tracker:
https://winscp.net/tracker/1015

martin wrote:

I'm bit lost as I do not see much difference between your two scenarios from your description.

Anyway to comment the log files:
lagant01@elearning.lagant.nl.log: This has MLSD enabled and I can see the .htaccess in the directory listing. So I hope you could see the file in panel for this case

lagant01@elearning.lagant.nl-1.log: This both MLSD disabled and Support for listing of hidden files disabled, as such it does not get .htaccess in the directory listing.

Maybe it was not clear in my comment, but the first listing was to show you that a .htaccess file really exists.
The second file (MLSD disabled) was the one showing that hidden files are not shown even when Support for listing of hidden files is 'On'. You asked me if it was on, and I told you it was. If you can see in the log that it was not on then tell me what I'm doing wrong because the program tells me it is on.
I've added a screenshot showing that it is on and you can see that the listing is not showing the .htaccess file.

I'm bit lost as I do not see much difference between your two scenarios from your description.

Anyway to comment the log files:
lagant01@elearning.lagant.nl.log: This has MLSD enabled and I can see the .htaccess in the directory listing. So I hope you could see the file in panel for this case

lagant01@elearning.lagant.nl-1.log: This both MLSD disabled and Support for listing of hidden files disabled, as such it does not get .htaccess in the directory listing.

martin wrote:

Do you actually have the hidden files set visible in GUI?
https://winscp.net/eng/docs/ui_pref_panels

If you have, can you attach a complete session log file (with Use MLSD command for directory listing = [pi]Off[/i] and Support for listing of hidden files = On or default Auto)?

Yes, this was really set in preferences and when I use the older version of Winscp or this version using MLSD it will show the .htaccess file in the directory.
I've created 2 logfiles, one with the LIST command and one using MLSD.
I hope this will give you enough information.

I've done the same on my computer still using the older version of Winscp and I saw that that version uses 'LIST -a' to list the files in the directory (as I thought it ought to be).
I also tried using Ctrl+Alt+H with this new version, but only my local screen (Windows) changes, the hidden files in Windows change form visible to invisible and back, but the remote screen doesn't change.

Do you actually have the hidden files set visible in GUI?
https://winscp.net/eng/docs/ui_pref_panels

If you have, can you attach a complete session log file (with Use MLSD command for directory listing = Off and Support for listing of hidden files = On or default Auto)?

To solve my problem with this site not supporting the MLSD command correctly I decided to install the 5.2.1 beta version so I could configure the session to use LIST.
After selecting MLSD as off I can configure the way hidden files are processed. I've tried every option but I don't see the hidden files anymore.
Is this a bug in this version or is it a problem on the server?

It's likely side-effect of MLSD support in WinSCP 5.
https://winscp.net/tracker/568

Most server's do not unfortunately expose information that a file is symlink, when using MLSD command to list directory contents, although the same servers do then using obsolete LIST command.

In 5.2 beta you can force use LIST, but I would not recommend that generally.
https://winscp.net/eng/docs/ui_login_ftp

After upgrading WINSCP to 5.1.0 (some time ago; I came from 4.3.2-1201) I didn't see it immediately, but recently I found out that symlinks on a Linux system were not recognized anymore when using FTP. The icon is not correct and when I remove a symlink pointing to a directory the members of the target directory are also removed. Today I installed the most recent version (5.1.4) and the problem is still there. When I search the faq'a and this forum or the realease changes using keys like 'symlink' or 'symbolic' I do not get any hits, so I assume that nobody else experiences this problem. Could this be a bug or am I doing something wrong? When I use my computer that has the older version of WINSCP on it, it works fine when connecting to the same server and processing the same directory.