Has anyone else had this happen? Before I go to bed, I click stop time on the options, and when I wake up all of my plants are dead and 3 or 4 hundred years old.

What's going on?

If you're leaving the game on the Options dialog or on the menu screen, you haven't actually stopped time. I've explained this issue more completely in this answer in our Support FAQ.

oh...thanks. That must be it. I didn't realize that.

Starting over once again because I lost almost all my seeds.

You shouldn't have lost seeds. The only "bad" consequence of not pausing is that the plants die. If they were pollinated, you can still gather the seeds and continue playing.

they weren't old enough to pollinate when I went to bed...and I was taking all the seeds I only had one left of and creating more...

oh well. I wasn't THAT far along yet anyways...

Oh, well that explains why you had to start over. I usually start a game to test something, and then get busy with other work and forget about them. I start over a lot!