[EDIT: It occurs to me some system info might be helpful. I am running Windows XP, Java 7. Also, was wondering about the OP name: J(ava) Gard(e)ner…and its relationship to the game!]
I tried running the game two ways and had a problem with seed throwing each time.
When I ran the game after clicking the jar (I do have a Windows system), throwing the seed (left mouse click) always threw for a long distance to the left. Right click did the same and did cause the mushrooms to fade.
When I ran via the .exe, the same thing happened except the throws were much closer to the tree (shorter distance). (Second try via .exe, the left throw was again a long distance and only to the left, regardless of which way I was facing.)
I think the sounds and music are reasonably good, but maybe a bit more tweaking is in order. I found the slow piano music a bit morose for this game. I think it is a very pretty piece of music, well written and solid as a composition, just not exactly hitting the right tone for the game. I can see wanting something peaceful, but maybe this can be achieved without what for me evokes melancholy.
Likewise the seed throwing seems like a near miss. And the “ungrow” maybe could be different from the “grow”? But I don’t know what I’d use instead.
You might rerecord your music sample, if you decide to keep this same cue. There are at least 3 audible clicks in it, two near the beginning and one close to the end that almost sound like lp record pops.
I like the menu system a lot and the way the game kicks off seems very promising and clear. It looks like a really neat concept for a game and I look forward to being able to grow my way past the first two-level obstacle. Congratulations on all you have achieved here!