Virtual Key strokes to Physical key strokes?

Question

I am writing a 3rd party program that tries to send keystrokes to this certain application using SendKeys().  The application is somehow able to realize these are virtual keys(probably noting that the input is coming from User32.dll), and is then ignoring them.  I was wondering if there is a way around this?  A way to hide where the input is coming from or, probably less possible, someway to send my virtual keys to the physical keyboard and then those to the application.