That scan actually looks very good on the peaks and abundance. I do see one major problem, turbo speed and HiVacuum. Turbo speed should be at 100% and the HiVacuum should be in the 10^-5 torr range not 10^-4 torr, that is too high. With such high pressure in the system the autotune is probably having trouble keeping things in the proper ranges. The turbo speed being less than 100% is either a sigh of a very large leak, super high column flow rate or a failing turbo pump or roughing pump.
What column are you using and what is the column flow setting?
Has the instrument gone through pumpdown?
Where you found the manual tune window there is also a Vacuum menu, what does it give if you select Vacuum Status?
I am having trouble figuring out how the source and quad temperature is up without the turbo speed being so low, usually that would trigger a vent mode and shutdown after a little while.
Where you are there scanning in manual tune, use the MoreParameters menu and use the Tune Parameters menu and change the 219 and 502 mass boxes to 28 and 18 and do a scan and see if your air and water peaks are higher than the 69 base mass of the PFTBA.
The only reason I can think that the HiVacuum would be so high if everything else is working corrrectly is if you are using Hydrogen as carrier since it doesn't pump as efficiently with a turbo pump.