I figured out the issue - In the past to simply create a reduced file for web with no watermark, I have used a blank png as the logo. I don't remember this plugin having a transparency option before so this was my solution. Now the blank png is causing the issue. Oddly though when I use a regular png logo the exact same size, there is no issue and it resizes properly.
So now I have found the solution but not sure why the blank png was causing the issue. Either way, thanks for your help and this great plugin 🙂