I've just updated the HeroMachine 3 Alpha so any custom colors and swatches your character has will now be both saved and loaded. Old characters saved prior to this release will not be affected in any way.
If you have a bunch of custom colors active, then you load a previously saved character, your current custom colors won't be overwritten with white -- only non-white custom colors from the saved character get applied. In other words, your custom palette doesn't get wiped out by loading a save.
What that means is, you could in theory set up a whole suite of custom colors that you use a lot, and then save that "character" as something like "Jeff's Custom Colors". When you start a new session and character, the first thing you could do would be to load "Jeff's Custom Colors", and all the colors you'd saved would now be active. It's a way of saving your palette between sessions.
I also changed the default size for "Save as JPG/PNG" to 500x750.
The "Save" box now goes away when you click "OK".
Finally, I implemented a small bug fix where the custom color picker was showing on top of the save/load dialog box.
Please let me know if you have any problems with the release, and enjoy, all you custom color creators!