Items with a green border signify that you don't have them.
Items in a recipe with an orange border signify that you don't have them, but you can craft them. (or you only have one of them, if only using dupes)
By default only duplicate items are used for recipes. This ensures you can keep one of every item. However, if having one of each item just isn't your thing, you can click "Customize" and check "Use all items" which should solve your issue. If you're still not seeing what you'd expect, send some feedback and I'll investigate!
Right now no recipes involving tokens are considered, so that's a possible reason you're seeing some things missing. Otherwise there might be a bug! Send feedback!
Aww man that should be fixed. Post about it so I can see what's up.
Darn. Okay well post on the forum. Just make a new thread and describe the issue.
I'll add more here as more feedback shows up and I find out what some common issues are