After testing with a clean installation of the Operating System using Windows 2012 R2, we are not able to reproduce the issue you are experiencing reason why we recommend making sure you are installing all the proper software and drivers for the other hardware components.
I've built a 2nd Server & experienced the same thing. It's not really an issue but an annoyance.
It's been tested & shipped to our client.
The next Server build I get I'll test it without the LSI card 1st & perhaps try an older firmware as well...