all files are uploading but index.php not?

I have been trying to upload files through the File Manager and was able to upload all the files but the index.php is uploading but not showing? The file size is 1.2 MB, is that the problem?

Possibly. While the general file size limit is 10 MB, there are lower restrictions on particular file sizes depending on what is a "normal" size for particular file types. I believe the limit for PHP files is 1 MB, but I'm not entirely sure.

Could you please try to reduce the size of the PHP file (either by removing some content, or by splitting it to separate files and use include/require to combine it) and see if that allows you to upload it?