Joe,
Any time you can inject a product into the body at the proper dose it will be better. I use the pour on for ease of animal movement through the chute. I don't see any bad effect from using the injectable as it is the same product just a different route of application.
One product which seems to be showing a bad effect on AI is a shot of Draxxin at time of AI. A number of guys have had bad conception using this product at time of AI.
One thing I will say is this is just reports from guys doing this at time of AI. There could be many other reasons they are having bad AI conception like stress, animal health etc.