don't understand...

are you sure the software is still availabe for patenting?

plus, the software was developed when you were the employee of the university with the sponsorship from your previous company. No matter what, they will be the owners of the patent (I assume that you are under the obligation to assign the right to your empolyer....which are common in U.S.) So, there is no way you can cut off their ability to use the patent.

Don't really understand what exactly is the problem you are complaining about...