Normally, you should run Wow Sales Reports (WSR) by double-clicking its excutable (after downloading and unarchiving it). You should see a black and white "dos-box" asking you for your WoW login name.
If that doesn't happen, or if you get any errors, you'll need to run WSR from the command line. You should also run WSR from the command line if you do not want to supply your login name.
How to run WSR from the command line
To run WSR from the command line, your need to get to a cmd prompt and launch WSR with two parameters, the first is the input (your beancounter.lua), the second is the desired output file name and path.
Like this wsr.exe c:\Program Files\World of Warcraft\wtf\Account\YourWoWLogin\SavedVariables\BeanCounter.lua c:\documents and settings\YourWindowsLogin\Desktop\someFile.tsv
If everything goes well you should see some scrolling lines (see second pic below) as WSR starts getting data from your WoW installation. At the very least you should see some lines representing errors.
Where do I find the output?
Normally, on your desktop. It should be a filed called AuctioneerData.tsv.
If you ran WSR from command line, you supplied the output path as the second parameter. If you have Excel installed, WSR will automatically open the output and make some reports for you.
What if I don't have Excel installed?