SpeedFan Query / Question

[Seanie's Show]

Hi guy's, first of all its been a while since ive posted here or messed about with my PC to be honest, Ive been playing about with my smart phone, rooting and modding it and its kinda taken over my life up until now, so im very sorry if ive posted this question in the wrong place.

up until now ive been using Gigabyte EasyTune 6 to control my fans but personally, I hate the huge, bulky UI, so ive decided to switch over to SpeedFan, I think ive configured it right and pretty much all seems to be working quite well, however I do have a couple of questions regarding the software if any experienced user can answer these questions for me I'd greatly appreciate it, but first i'll post my system / fan setup.

Im running a Gigabyte G1 Sniper 1366 mobo, it has 5 PWM fan headers on it, all of the headers are taken up with fans and all 5 headers are monitored and reported in the bios, they are labelled CPU Fan, Sys Fan, Fan 1, Fan 2 and Fan 3, however, on fan header 1 is my water cooling pump which registers as 4440 rpm in the bios but speedfan isn't seeing it, speedfan says 0 RPM and the same for fan header 3, does anyone know why ?
My Noctua Fans are connected to the CPU header, the Evercools are connected to fan Header 2 and the other noctua is connected to Sys Fan Header, seems to be header 1 (Laing DDC) and header 3 (Coolermaster) that speedfan cant monitor.
(See attached pictures)

ET6 could see and monitor all 5 headers, whereas SpeedFan doesn't seem to be able to monitor all 5 although it can see them, if I cant resolve this, i'll end up going back to ET6.

Ive also attached some pictures of my config setup, however at the moment I have had to configure speedfan to also control my 2 graphics card fans, I would prefer the ATI software to automatically control these for me as it did before, how do I set this up ? I tried selecting auto for the fan config in speedfan, but they didn't appear to speed up at all when I ran heaven benchmark, I had to quit the benchmark quickly and manually ramp the fans up to cool down the cards, at that point is when I configured the fans manually in speedfan for the 2 x GPU's.