Tracking things planted using seed bags is sometimes imprecise. Avoiding jumping, combat actions (e.g. healing yourself, even HoT ticks) in the ~1s period around using a seed bag for best results.

Harvesting bursting plants should decrease the amount of that plant Spade thinks you have; not sure if the behavior you described in the second case is a problem (sounds like it decremented correctly, but then did not figure out that you re-planted it?).

If Spade thinks you have crops on your farm that aren't there, it will not correct itself. Run /spade clear (ideally when your character's farm is empty) to reset data for the current character.

I think this is largely addressed in version 1.6; I've included my thoughts on the implementation details below.

Spade will now display seed bags. It does so in a separate ring, partly to reduce the number of things you might have to sort through to pick out the bag/seed you wanted. If you've got both seed-purchased and gold-purchased bags of the same type, it'll only show one of them in the ring (preferring the one with the least charges remaining); if you've got multiple bags of the same type and purchase type, you're in WoW's hands as far using the right one is concerned. I'm slightly unhappy with using an alt-click on a tilled soil patch to open the ring of seed bags -- you'll have to target an AoE spell after you select a bag, which makes placing the mouse over a Tilled Soil patch a senseless complication -- so you're able to configure an alternative binding for that ring using OPie's binding panel.

Tracking things you've planted using seed bags is difficult, as the game provides addons with no unambiguous indication as to how many tilled soil plots you've targetted. The mechanism used to determine this in 1.6 may be too imprecise to work in the long run; if that proves to be the case, Spade will probably have to switch to requiring you to sweep your mouse cursor over all of your plants to track what you've planted. In any case, I'd like to hear how Spade 1.6's seed bag tracking works for different people.

Seeds and seed bags used to plant things to complete Work Orders should also be highlighted in Spade rings with a quest exclamation mark. This one is relatively straight forward, and should just work.

In theory, Spade does have that data, so it could show it. In practice, I'm somewhat worried about the length of that tooltip if you have a fair number of characters on one realm -- it might get too long to work properly.

Install, update, or enable OPie and then restart WoW.

Version 1.5 improves the tracking of Bursting plants. If that white turnip is still haunting your list of plants, you can use the /spade clear command (preferably when your character's farm is empty) to erase Spade's memory of that character.

Jogu's prediction is now remembered and shown in the /spade tooltip. It could be nice to relate those hints to actual plants, and show you both today's and tomorrow's crops of the day, but those are features for another day.