There are real differences between Lightroom and CS3 images. I believe part of the reason is their different user interfaces; for me, this can result in slightly different outputs. I navigate and work within Camera Raw differently from how I navigate Lightroom.
Even when I was using Camera Raw 4.0, there were differences between outputs, even though it is said that LR and CS3 both come with CR4. Even though adjustments in Lightroom are essentially compatible with CR4, Neatimage 5 profiles (which were created from Lightroom processed RAW files in PS3, for removing noise from LR imported images), I would ALWAYS get a lower profile match with CR4 processed files-- this alone was interesting, because I bought into the idea that they processed files the same. There were even subtle differences when comparing zero'd, linear results from LR and CR4. If there aren't subtle, technical differences between the two engines, I still believe that the different user interfaces affect the end results.
This is not to say that you can't produce visually identical results from LR and CR4, but my personal experience has shown that it is entirely possible to produce different results.