I have never posted on any forum before so bear with me.

I know there are a bunch of posts out there about saving problems with the creation kit, but none of them seem to cover my problem. I load Skyrim Master File, Frost fall, and Extended Scroll Crafting which I set as active.

I copied his scroll recipe file and attempted to change it to make a frostfall spell scroll using the same principal. Everything looked good, and I hit save, the little asterisk went away from the top and I closed the Creation Kit assuming it was a-ok. When I went in-game to test it, the recipe did not appear so I brought Creation Kit back up and loaded the same things, the same way, I see my recipe there, but when I click 'edit' I find all the values are gone, I can put them back in and it appears to save fine, but its still gone next time I bring Creation Kit, I have tried moving the .esp file out of the folder and back in, and I have tried running Creation Kit as administrator, neither had any effect, not really sure what to try next.

Welcome. If the Recipe is using Frostfall resources you'll have to make it a master of the ESP you are saving. Otherwise, once you save the ESP you are basically telling the CK to remove any resources that ESP doesn't know about, and this is why your changes are gone on subsequent loads.

edit: note that the above isn't really good modding practice, it's just to explain how this resources business works.