I have been bitten by the "not so smart retract" and have learned that "always retract" is your Friend when using the rough and finishing routines. The time and travel saved with the smart retract is not worth the cost of an expensive mold cavity or core with gouges created from abad smartretract.
It is still doing it in the latest version of Creo I found out the last time I forgot to change the smart retract to always. I really need to change my site files to say always retract if I can rather than relying on my fading memory.
Good luck with your Implementation of new startparts,solid tools, site files and such. I have all that and it works fairly well for me with the occasional glitch usually from the solid tools or my automated cam sheet(drawing) that gets sent to my operatorand it usually comes from the cutting parameters not coming in correctly (totally my fault). I then just adjust the parameter manually in the sequence then write it down and attempt to fix it when time allows. Keeps me busy most of the time.
By the time you are done implementing all that Creo 3.0 will be out then you chase new bugs around !!