Yes, I've had this in the past and I've also always been annoyed by the fact that the position that the user prompt dialog appeared was never entirely predictable.
As a consequence of another thread on this forum I now use this approach that prevents these issues. I always execute a sub macro prior to executing the Prompt for User Input action - a bit like this:
The sub macro which I have named [LIB]_Center Keyboard Maestro Prompts and Alerts positions the following Prompt for User Input dialog consistently. It looks like this:
