I updated the tags and moved this to Mass Spec for better visibility. Have you been able to resolve the issue?
We have seen something similar to this before and it turned out the brass nuts source was slightly loose. so when it tries to ramp, vibrations distort the ion "beam" and it can't resolve the peaks when ramping.
Try dissembling the source, check the entrance lens for any debris and the n reassemble it and ensure the entrance lens and other parts do not move when "wiggled" a little.