I can see a large file have been uploaded. Now I need to check-in/Publish. Why is it taking long time to check in since the file blob is already in the SP? Then it's finally times out.
Can you try the following -
1.From your site select Site Actions - Manage Content and Structure
2.Navigate to your checked out file(s) in a directory.
3.(Optional) Multi-select files by using the checkboxes at the far left.
4.In the toolbar, select Actions - Publish. Or, using the drop down menu for the file, select Publish.
Your file should be checked-in, approved and published all together.
Hope this helps. :)