Inkscape is a great free tool to use in order to manipulate SVGS, but it does have its fair share of quirks. One thing that sucked away a lot of time for me was figuring out how to make it stop adding a transform to an object once I started to move or modify its scale in anyway. I typically just take the path information from the SVG and then use that for my programming exploits. Having to worry about a transform just makes my life a lot more difficult than it needs to be. After doing a LOT of searching through forums and StackOverflow, I discovered a couple of solutions. I feel its my obligation to share this.

Make sure the Object is in not in a group layer

If the object is nested within a group, Inkscape will automatically apply a transform. So to fix this, just hit Ctrl + Shift + X to bring up the XML Editor. Once it is up, just find the svg node in question and pull it out of the group. This should fix the problem.

Convert any shapes(Circles, Squares, etc) into paths

I thought I was good with the just the first solution, until even after doing that, I noticed some objects were still applying transforms. After more researching, I discovered by accident that the problem is actually the fact that if the object was created with the Inkscape shape tool, then no matter what, if you modify that shape, Inkscape will add a transform. To eliminate that, you just have to convert the shape into a path by pressing Ctrl + Shift + C. Once you do this, you should be able to modify shapes without worrying about transforms being added.