I attempted to reproduce this on our test bench, but I was unable to with:
Windows 7 on an SSD
PrecisionX 5.2.3
X79 Dark
GTX 760 with ou without an overclock profile
I tried having it start with Windows both minimized and not, with and without a profile loaded, and I had no delays at all with startup in any way (launching program, typing, hangs while something loaded, etc.).
I would suggest uninstalling PrecisionX, then navigating to Program Files(x86)>EVGA and deleting the PrecisionX file, then reinstalling PrecisionX and see if that helps at all. There may be an old file that's gumming things up. Don't forget to write down any setting you put in PrecisionX, as you will lose them doing this.