Well, if you want to remove all the seeds listed in the VST, then u have to delete the VST file.
Follow these steps to delete the file:
>> Goto My documents
>> There should be a folder called LDW, open it, then open the plant tycoon folder
>> then delete the VSTray2*
* This will delete all the seeds u have in ur game2
Now open the VST, you should have no seeds for the second slot.
& i hope u'll do it correctly!