thanks for the report, M.Asad
try this: close plant tycoon completely, then run VST, in order to see the latest happenings in your PT game. This is because PT saves the game approximately every ten minutes or when you close PT.
having said that, when i was writing VST, i found the problem you are discussing. i started a new game and wrote on paper all the new species i discovered and when VST finally said i did not discover a plant that that i knew i had discovered, i checked the total number of species discovered in the plant tycoon stats and found that number to be lacking by one. plant tycoon for some reason did not yet count that species yet. i believe eventually plant tycoon did mark off that i had discovered the species, and when that happened VST also reported it as having been discovered. since VST only reports the species that PT flags as being discovered, even if you have the plant growing right there on the main page, VST will report it has never been discovered.
thank you for testing the beta version! anything to report, good or bad, regarding seed loss?