Releasing libraries used in a commercial application as GPL

While I was at university I developed some PHP libraries which I intended for personal use. I used them in a few personal projects.

When I joined my current job we created a commercial product which required the same functionality. I proposed using my libraries as they were familiar to me. We did.

Since then I have modified and improved the libraries in the last couple of years (all in my own time) and want to release them as open source under the GPL licence.

Now under the GPL licence you cannot use the libraries as part of commercial software, so does me doing this now in any way affect the commercial software or their protection? Am I free to release these libraries in this way?

Thanks in advance!