After looking through the .json for vanilla MC in the agricraft config, it seems that the mutation for sugarcane was changed to beetroot and wheat (or beetroot and carrot, can't remember--not home right now). I think this may be a result of Pam's harvestcraft (however I haven't tested it without), but it seems like the beetroot seeds aren't implemented properly, making the mutation impossible and not showing in JEI.
On a similar note, none of Pam's seeds can be used with agricraft, this is because the json files use the item ID "artichokeseedsItem", when the correct is "artichokeseedsitem". I think that pam's beets are overriding vanilla's in the mutation, and since they aren't implemented properly, the mutation can't be done.