In GUIDE, one of the first things that is done by the function that has the same name as your .fig file, is to test to see whether it is already running, and if so then it does not create another instance. You would want to disable that code. My vague memory is that it works by looking for a figure with its own Tag.
There is no inherent problem with running several figures with the same Tag. You will need to check the rest of the GUIDE code, though, as I seem to recall it using the Tag for something else, possibly in the closing function.
There is a potential problem if the generated code uses Tags in order to locate items without qualifying that those have to be part of the same figure. I do not remember seeing a problem along those lines come up, but I have not looked through much GUIDE code.
