What is the oven temperature during that run of the baseline chromatogram?
Is there anything above 44m/z in the background at the 8.8 minutes mark you have displayed?
If that background is entirely what is displayed in the spectrum window and the background is 300,000 counts, what is the electron multiplier setting during that run?
From looking at the spectrum and the mass counts there, it would appear it is mostly the m/z 28, 32 and 44 that is giving the 300,000 count background. I notice the Autotune spectra has almost 3,000,000 counts for 69 at 1859 volts on the electron multiplier. That is super sensitive, we normally run with 69 at anywhere from 300,000 counts up to 800,000 counts. You could probably drop the multiplier voltage down to 1600 volts and lose most of that background and the spikes would barely be visible if at all. They could simply be some electronic noise with the gain set that high which is not unusual for an older instrument like the 5971.
Try backing the voltage down until you have only 28, 32 and 44 appearing in the background with a threshold of about 100 which should be when you get the 69 below 500,000 counts, and see if you notice the spikes then, and you will probably gain better signal to noise ratios between your background and your target peaks, even though the total counts will be lower, which will give you better low end sensitivity and more linear range for the analysis.