So based on what’s been described so far, chances are that during the install the administrative mode was chosen which set up a Windows Service for auto-starting Syncthing when Windows starts/boots up.
In Windows, for security reasons the Windows Service user account runs with restricted privileges which prevents it from accessing user data (e.g. your D:\ partition).
One solution is to grant the Windows Service user access to your files and folders: https://github.com/Bill-Stewart/SyncthingWindowsSetup/?tab=readme-ov-file#granting-folder-permissions-for-the-service-account
However, a simpler, more secure, and more portable solution is to run Syncthing as the same user who owns the files and folders under D:. It ensures that all files and folders that Syncthing creates will also be owned by the same user. Upgrades of the Syncthing executable will also be simpler.
It doesn’t sound like you have much of a Syncthing setup yet, if so, then the easiest path forward is to uninstall the “Syncthing Windows Setup” package, reboot (for good measure), and then reinstall using the non-administrative mode.
If uninstalling and reinstalling isn’t an option, the Syncthing Windows Setup page you link to has all of the info for manually making the necessary changes.
In Windows, if you right-click on the drive letter and select “Properties”, the dialog box will show the filesystem being used. Given what’s known so far, it’s likely NTFS.
There are various reasons for using one filesystem over another, but for most users it’s a combination of maximum file size, maximum volume size, and portability. USB flash drives are commonly formatted with a FAT filesystem because it’s usable out-of-the-box with Windows, Macs, Linux, Chrome OS, Android, iOS, etc.