First: If the project was under the the GPL and the libraries are under the GPL, the result must be under the GPL.
Second: Depending on where you live, you might or might not have given over the rights to your employer. You need to take your contract to a lawyer in your country and ask them. As usual, slashdot is _not_ the place to get specific legal advice; we can just blabber about generalities.
Thing is: The GPL does not matter unless you distribute the software to anyone. Before that, the licence does not matter. So you need to check the _second_ point first. When/If you release the software and the libraries are GPL, it's a clear-cut case.
No idea if your employer can go after you for "wrongfully leading them to believe they owned this stuff" though...
"When the going gets tough, the tough get empirical." -- Jon Carroll