Indeed I've noticed the short flip mistakenly treated as long flip problem too, but not very often so I thought maybe it was a mistake of my hand. But since you are reporting this problem too, I'll try to see if it's really a bug.
This might help you pin point the problem:
- I've noticed the described behaviour with the normal page mode as well. Have you changed any code that is used in this normal mode?
- In the normal page node, I've noticed that flipping forward from say page n, it brings me to n+5. Going back and trying again (with a short flip), the same happens. I have also waited for a while, but again it goes to n+5. If I exit the document, go back to page n, flip the page, it goes to n+1! Very strange.
- It seems that this behaviour occurs more frequently if I flip pages fast. If I wait a while on each page it seems to occur less frequent. Also very weird. Makes me think I should go to bed more early!
Anyway, I want to complement you again, because reading scientific articles was almost impossible.
As for the skipping over problem, I intend the algorithm to skip margins only.
OK, this sounds reasonable, and indeed seems to work most of the time. I had one other idea which helps reading papers where there are different even and odd page margins (see attachment for an example). The following alogrithm could help: when finishing one column, go to the next by panning the width of the column iff there is enough space on the page. If not, then the right hand margin of the column is placed against the right hand margin of the page. This condition is only met if the zoom factor is more than 50%. So normally, you wouldn't notice it.