What went wrong here

Just trying to leearn what I did wrong.I did the Delta Glider-ISS tutorial in the manual (page 73-74). I have done it without problems before a few times, but this time it didn't work out.I followed the checklist. I got up into orbit, got a nice circular orbit, and did the align planes bit and got inclination down to about 0.1% or so. All was fine until it was time to sync orbits. Usually, I get an intersection at Intersect 1 or Intersect 2 like the manual sais. This time however, I didn't. The manual sais that if I don't get an intesection, I should set the MFD to Sh Periapsis instead, so I did that. I then got Sh-ToR(3) and Tg-ToR(4) to match (they lit up yellow and were pretty close). So, I just went around the earth a few times rather than making a longer burn and mess up the orbit. However, when the orbits did intersect, I was much higher than the ISS. It was like 900K away or something, right below me. I proceeded with the checklist in the manual, but I had to fire the engines a LONG time to get near the ISS. When I was getting close, about 400K, my orbit was so messed up that had I not paniced and corrected it, I would have gone through the atmosphere and probably burnt up. Is the manuevre different when you have the Sync Orbit MFD set to Sh-Periapsis instead of Intersect 1 or Intersect 2? Did I do something else wrong?