It may hit slightly lower in Latest, and therefore be slightly less likely to get as many views. The key factor is how long ago you generated it (the longer ago it was generated, the lower it will appear). It's usually best to generate memes immediately before you submit them, to get the best position in Latest (ie, remake comments into memes before submitting them).
But having said that, it's not a big deal. I think imgflip releases memes every 15 minutes now, which means more frequent and smaller batches (so position is not as much a factor).