I'm not entirely sure what's happening with your game. The gardening skill cheat seems to be working of me. So my suggestion is to try this out in a test-new game.
In live mode, press Ctrl-Shift-C. Then highlight copy and paste (by pressing Ctrl-V together) this: stats.set_skill_level major_gardening 4 into the cheat console.
I started with Sims that had no gardening skill and skilled them up to Gardening 2, Gardening 4, then 6. Each time it worked.
If it ends up working in your test-game. Then go ahead and try it in your main game.