Hi Mulveyja,
Thank you for your interest in Syncfusion Essential Diagram.
I am afraid, I was not able to reproduce this issue with v4.2.0.37. I have attached my test sample here for your reference. In this sample initially you should select the symbol and you can enter the X and Y coordinates(10,10) in the corresponding textboxes and when you click on the "Ok" button the inner rectangle will move to its corresponding modified location within the symbol.
Please try this and let me know if this helps you.
Thank you for your interest in Syncfusion products.
Regards
Nagarajan
CustomSymbol.zip