People often suggest a Hiit routine where one alternates 1 minute at 60% Heart Rate with 1 min at 90% Heart Rate or whatever but I find that it takes me almost a minute getting from 60% HR to 90% HR and another minute in reverse.
Therefore if someone recommends doing say, six cycles of 1 min at 60% and 1 min at 90% for a 12 min routine it would actually take me 24 minutes!

i.e. 6 cycles: 1 min getting HR from 60% to 90%
1 min with HR at 90%
1 min with HR coming back to 60%
1 min with HR at 60%

How do other people factor all this into their routine or am I understanding the HIIT method all wrong?

Many Thanks

One minute High Intensity Intervals is not high intensity, it is interval. The suggested time is like 15-30 High Intensity to 1-2 minutes "resting/recouping". After 4-6 you should feel entirely exhausted. More info in HIIT forums.

Exactly, and heart rate is a poor way to "measure" HIIT. The high intensity interval should be as hard as you can possible do, and the low intensity interval should be a very easy jog or even walk, as low intensity as you can do without stopping moving completely. Obviously your heart rate at the start of the high intensity interval will be low and should only reach near maximum by the end of the high intensity interval or even after the start of the low intensity interval.