Is a partial PhD a liability in a job search?
It's possible that they're not taking you as seriously as you would hope because they think you might want to make your PhD the priority and quit the job soon and return to academia. Or, they may see you as non-committal—one who jumps careers—and they are looking for somebody who will stay with them. 

Also, software engineering is a hot field right now. There might be a ton of other really stellar applicants, so you might be facing stronger competition than you expected. 

Of course, it does depend on a host of other factors, some of which are in your control and most of which are not.