Right-click the file without a thumbnails, select the Control panel option under More options. You will find in there troubleshooting tools which will help you find out what happens behind the scene and where the problem might be.

1. Use the Thumbnail generation section to see which command is being run.
2. Copy the executed command and try to run it directly from the command line of your server. Observe the error and take appropriate actions to correct them.
3. Make sure the folder the image files are in, are writable by PHP. FileRun needs to cache the generated thumbnails in a hidden folder next to the files. If the folder should be read-only, then configure FileRun with an external location for the thumbnail cache (see $config['path']['thumbnail_cache'] on this page)
4. For PDF files: make sure that Ghostscript is installed on the server and working.
5. On Windows servers: make sure PHP can run external applications. You need to give the Internet Guest User (IURSR or IUSR_<your-computer-name> on older servers) “read & execute” permission on the file that PHP is trying to run ImageMagick trough. That would be “cmd.exe” (located usually inside the folder “C:/Windows/System32”), the file used for running programs trough the command line.
6. On Windows servers: you might also need to adjust the permissions of the system temporary folder, to allow ImageMagick, Ghostscript and most importantly IUSR to write temporary data in there. Without the permissions, generating thumbnails from the command line might work, but it won't work for FileRun.

Still having troubles? Post your troubleshooting output on the public forum and you will get help: https://feedback.filerun.com