Well there are a couple things at play here:
1) I do a sort by size, which I don't think is the issue if all your sprites are equally sized. However if you remove the call to Sort on line 286 of SpriteSheetPackerForm.cs you should see if that makes a difference.
2) Because the tool does some iteration to try and optimize sizes, and because it was developed with the ability to handle lots of different sized images, it's not guaranteed to ever arrange sprites in any given order, hence the creation of the text file to tell you where each image is.
If you're just building sprite sheets of equal sized images and know more of how you want them arrange (e.g. number in a row, number of columns, whatever), you might be better off making your own tool. This tool is really targeting the problem of packing lots of different sized images. You're more than welcome to use the UI code and any logic from this tool in building yours, but I have a feeling the packing logic this tool uses is somewhat at odds with your goals. You could more easily make a tool using a packing algorithm like this:
- get number of images in row
- figure out number of rows
- get image size
- create new image of the right size
- do a couple of nested for loops to draw the images into the output
- save the output file
All of which is vastly simpler than what this tool's logic is and would be guaranteed to produce files that meet your requirements.