That would require to know the layer structure of the AI file/ converted shape layer groups. Presumably there is some random leftover path or point somewhere that affects the bounding box and hence all transforms.
I hate to be that guy but I've looked everywhere, but I can't seem to find any issues with the illustrator file. I think something is happening when I convert the vector to a shape layer.
Here's the vector file in case you are interested. If not I rest my case.
I looked at the illustrator file and opened the US-EPS-01-0002.ai file and found that it only had 3 layers, copyright, US and background so I selected the US layer and used the Release To Layers Build which gave me new layers named layer 4 through layer 54. I then selected all of these layers to drag them above the copyright layer, saved the AI file in the latest format, then imported as a comp retaining layer sizes. I opened the comp, selected all of the layers and revealed the scale property and scaled them all down uniformly about 10%. Everything worked just fine. I went back to the original scale, selected all layers and converted them to shape layers then selected the scale property and scaled them all to 90% as before. Everything worked fine.
This make me assume that you did not release to layers but instead converted the single layer map into a bunch of shape layers. I checked that theory and found that the anchor point of the New York group (group 34 in my test) was not in the center of the state. You have two options, move the anchor point manually before you scale trick, which is very difficult because you'll also have to move the position of the group 34 transform controls, or use my technique of releasing to layers, importing the .ai file as a comp retaining layer sizes and going from there. There's something about the original path for the NY paths in the original file that cause the shapes from vectors to put the anchor point of that path way off to the side. In any case, releasing to layers is a better workflow that will give you a project that is easier to edit by far.
yep that did the trick! Thanks you so much!