Some files not visible (NOT CTRL+ALT+H)

I've recently updated to 5.5.1 and have a strange problem.
I am connecting to my RasPi and can't see some of the files.
Those are NOT the .filename files I am talking about. I am aware of the CTRL+ALT+H function and it is switched to show those files.

Also the rights seem not to be a problem because I see files with the same rights as the ones that are invisible.

In this case some of the files are .tlc or even .txt files.

I could see all the files with an older version of WinSCP.
The files exist I can see them when I login through console and ls.

Can somebody help me out here?

Please attach a full log file showing the problem (using the latest version of WinSCP). Note name of a file(s) that you are missing.

Well...what should I log there?
I just log in and there are files missing.
So this is what the log looks like:

<?xml version="1.0" encoding="UTF-8"?>
<session xmlns="https://winscp.net/schema/session/1.0" name="zensored@zensored" start="2014-02-05T19:29:10.264Z">
</session>

Files that I miss in that folder are for excample:

8ball.tcl
CONTENTS
alice.tcl
autogreet.tcl
autogreet.txt

and so on.
As you may have recognised, it is the scripts folder of an eggdrop. This is where I realised the problem but it occurs on other folders also.

As I have mentioned above: the permissions are not the problem. Files with the same permissions are visible.

I need a session log not XML log.
https://winscp.net/eng/docs/logging