You can reload QlikView from the comandline, using the suffix /r. IE if you type
c:\Program Files\QlikView\QV.exe /r "d3test_loading.qvw"
From the command line, in the same folder as d3test_loading.qvw it will reload and save that file. You can also pass parameters through the command line.
This means you can set up a batch file (or a call through some programming language script eg VB) and schedule that, either through publisher or windows scheduler on your server.
However,as Saravana mentioned I would not recommend this as
a) it is not as secure
b) you do not get the log files, or error detection
c) you can't do things like add categories, or ad groups or section access etc that you can via the publisher.
I think you should find out what the problem is, and check that first though!