I don't think this is a problem with image joiner, more AGK. You will get these issues if you do not adhere to ^2 image sizes. If you use any other size, AppGameKit will pad out the image to the nearest ^2.
Quote: "So I hear you say, where is the problem, create all your sprites at an even size!!!
Not so easy when you have over 300 different sprite files!"
Yes it can be a pain, as you can't always resize an image to the correct size, without badly altering the aspect ratio. I had the same issue with a few projects I started when AppGameKit came out. Adding clear borders to get all the off size sprites the same size and keeping the sprites centralized was tedious work, but I got through it with patience.
The setdefaultmagfilter and other commands do change the way images are treated, but will not fix the problem with non power of 2 sprites. If you set the filter type to 0 you will have a sharp but blocky look to your sprites. If you set it to 1, it will filter the sprite to look blurry. I tend to use 0 as I prefer the sharp look in general. If your graphics are fairly high res though, the blurred look can look better.
Try a changing a couple of the offending sprites to a ^2 size as a test and see what happens.
Oh another thought that (may), help you without having to edit the images. You could try the SetSpriteUVBorder( iSpriteIndex, border ) command.