First off, what version of S3D are you using? They broke the crap out of it when they went to 4.1. I had a feeling this would happen and never upgraded.
Go to S3D forum as there are so many bugs you are wasting your time trying to understand why it is doing something if it is a known issue.

And you are correct, if the tool path for layer 5 and layer 6 are identical, the the tool speed should be identical. Perimeter will be slower if set to default. If there is an area of bridging within the layer the speed may be different during the bridge if the bridge speed is set differently, etc. But the over all pattern will be identical between layer 5 and 6 in this example.
Could also be a mechanical issue with the printer..