You are referring to the hyperspace translation times, which is a very different thing from what kaplishkap011 is describing, which is the supercruise lag which affects AMD video card users.
For the hyperspace translation time issue, switch mode, whatever you are in, pick another mode, and it will clear up, then you can switch back to your preferred mode and it should stay cleared up. This isn't a new thing, it's been around for a bit and that's the fix for it.
kaplishkap011, you are welcome, but the real thanks goes to Genar-Hofoen and the others on that thread I linked who've spent so much time tracking down the issue and the fix and posting that fix.