Yes, it is all in your head. I am sure the throws are shorter. You should have measured the throws before and after. Maybe someone else with a 128i 6MT can pos their shifter throws from 1st to 2nd. For instance on a 135i with the N54 the standard shifter throw are 80mm vs 55mm for the Perf SSK. N55's have a 70mm shifter throws. It doesn't sound like much but the Perf SSK for my N54 is really sweet & short!
And yes, when the SSK is new... its quite notchy. Especially when the trans is cold. After a few thousand miles... it will loosen up some. but some notchy(ness) is to be expected. Your fulcrum point has change, so it will be harder to more the shofter arm.
Here are some good side by side pics of an e60 SSK on a e39. What is important is look at where the fulcrum point is(ball pivot) vs the stock shifter.