An update for anyone who may experience the same as I...
the changes I make to my keymaps are saving.
however, when I select file -> open -> Profile then look at my Key Maps tree, I have five keymaps with mapped keys in subtrees. Below these I have some empty keymaps with no mapped keys defined at all. If I right click and choose delete on these empty keymaps they disappear from the list.
At this point I select file -> Save. And then exit the program, if I re-open after doing this, those empty keymaps are back as tho I had never deleted them.
Upon further examination I figured out what was happening, those keymaps that I had deleted still had a character set assigned to them, so after removing the character set from the keymap then deleting them they are now gone if I save and re-open ISBoxer.
This is a nice feature, as it is preventing the accidental permanent deletion of effort.
Sorry I wasn't as clear and concise as I should have been Lax, I should have paid better attention to what I was doing
Thank you for the incredible attentiveness you apply to your product, you are indeed one of a kind my good sir and I appreciate the ease with which you've made multi-boxing accessible.
Keep up the awesome, you excel at it!