Steps to Reproduce:
touch a and touch A in the project folder.
Does this issue occur when you try this locally?: No
Does this issue occur when you try this locally and all extensions are disabled?: No
I can confirm this. Same version, same issue.
When I ls the files in terminal you can see 2 of them: makefile and Makefile, but in the tree only the makefile is visible.

I believe we always had this issue. Let me know if this was working in previous versions, and if yes please specify which.
Same name different case has issues across the workbench, not sure if this is explorer specific @bpasero fyi
🤷♂️
I thought it is a very special case to have files with the same name but different case, but in fact it is not so rare.
If you have a folder called Program and a file called program inside it, and you want to move the file outside the folder in vscode, you will end up finding the file disappeared
I have same issue with folder name, where it is important.
Executing a composer install on a Laravel project, some libraries where originally registered with lowercase vendor name, and some other with uppercase.
Right now all the libraries in the uppercase vendor folder are invisible for us. It is not just one file missing, is a whole set of libraries.
Workaround is use the "add folder to workspace" menu option, and there you can see and correctly select the uppercase folder name to be added in the root of the workspace. At least that way we can see them.
Windows 10 supports case sensitivity per directory [1], I believe Visual Studio Code and Remote SSH should default to a case sensitive workspace on Windows 10 whenever possible. I just got bit by this in a deployment. To make matters worse, I can't rename 'gamma' to 'Gamma' if the 'Gamma' folder already exists but is not shown inside of Visual Studio Code:

[1] https://devblogs.microsoft.com/commandline/per-directory-case-sensitivity-and-wsl/
Should be fixed via https://github.com/microsoft/vscode/issues/48258
Please try out vscode insiders from tomorrow
Does this work now as expected with vscode insiders?
Thanks!