Don't forget about the mouse aim dead zone added in the steam version.
The behavior in the first video you posted looks the same as the problem I had with my mouse. Your mouse may be failing to register clicks properly. My mouse before I fixed it would often double click, do nothing, release a held click or release and bring it back even though I was still holding the button down.
Try binding fire to your key board.
As for fixing the mouse the problem is an electrical build up on/with in the mouse. You must discharge this some how. Just taking the mouse apart and touching the insides seems to be what does the trick so long as you discharged yourself first. Many people think it is a problem with lubrication or the clicking leaf springs as I did but that is ussually not the problem. Messing with those things discharges the mouse thus people think one of those things was the problem when in was really a static problem. This is a common problem with logitech mice.
Oh and note that the pulse rifle has an overheat feature, it stops firing when overheated. I don't think you can fire all 99 shots in one go. I would have to check but I think it overheats after 40-50 continuous shots.
To fix the mouse aim in steam version (only version I have for windows) I am using this
http://homepage.eircom.net/~duncandsl/avp/ which only fixes it while standing. I think the dead zone is also present when using the predator's zoom. Wall running I think is ok.
Beware though that renderer is crash happy.