I'll try to debug this. Please provide me an email address, so I can contact you for further details, once I get to it.

martin wrote:

Sorry I didn't make it clear. If you look at my previous post. There are two directories under a main directory and each one contains "style.css"(the content of the two files are different). What happens is that it asks me if I want to overwrite, if I choose yes, then there are two copies of the same file(whichever is transfered later). If I choose no, the transfer is correct.

Do I understand right that if you choose "yes", both directories will contain copy of the same file (same version of style.css)?

Yes, exactly

Sorry I didn't make it clear. If you look at my previous post. There are two directories under a main directory and each one contains "style.css"(the content of the two files are different). What happens is that it asks me if I want to overwrite, if I choose yes, then there are two copies of the same file(whichever is transfered later). If I choose no, the transfer is correct.

Do I understand right that if you choose "yes", both directories will contain copy of the same file (same version of style.css)?

martin wrote:

It is SFTP. I am dragging the dir inside the winscp interface. I believe the box is from winscp because its got lots of buttons there.

And are you sure that the local file, you are asked to confim overwrite of, does not exist? Maybe I miss point of your problem.

Sorry I didn't make it clear. If you look at my previous post. There are two directories under a main directory and each one contains "style.css"(the content of the two files are different). What happens is that it asks me if I want to overwrite, if I choose yes, then there are two copies of the same file(whichever is transfered later). If I choose no, the transfer is correct.

It is SFTP. I am dragging the dir inside the winscp interface. I believe the box is from winscp because its got lots of buttons there.

And are you sure that the local file, you are asked to confim overwrite of, does not exist? Maybe I miss point of your problem.

martin wrote:

What protocol, SCP or SFTP? Where do you drag the files? Inside WinSCP, outside? Do you have drag&drop shell extension installed and turned on? Is it really WinSCP who asks for overwrite, isn't it box of Windows Explorer?

It is SFTP. I am dragging the dir inside the winscp interface. I believe the box is from winscp because its got lots of buttons there.

What protocol, SCP or SFTP? Where do you drag the files? Inside WinSCP, outside? Do you have drag&drop shell extension installed and turned on? Is it really WinSCP who asks for overwrite, isn't it box of Windows Explorer?

The problem happens when I transfer a whole directory from remote to local. It sometime asks me if I want to overwrite the file???. Say I am dragging directory "remoteDir" from remote to C:\. The directory "remoteDir" is like this:
<remoteDir>
<dir1>
index.html
style.css
<dir2>
index2.html
style.css

It asks me "Do you want to overwrite style.css?". Is this a bug or I am not doing something right?