Arjun from Lightroom support helped to resolve the issue. I had to remove all the already sync images from Lightroom. Then I had to upload all new raw images via web page. Lightroom app was not responding properly, so I had to do it via web page. Seems it's a bug from the app, need to be resolved.
Where are the raw images located that you are uploading from on the iPad? If they are in the Photos app (camera roll) you should turn off your iCloud sync. With iCloud sync on, the Lightroom upload sync is competing with the iCloud sync.