Hi-Z input issues using plug ins

So I’m using an Apollo twin interface. Plugging straight into the HiZ input on channel 1.
Was always getting some nasty overtones when I recorded. Like the amp tones sounded 90% great but every so often I could hear particular notes… feedback, I think is a good word. This very harsh overtone. It made my playing sound sloppy (which it might be lol) but more then usual. Signal never clipped or anything. The pre amp level was basically at zero.
After many hours troubleshooting. I moved the input to the back (not HiZ) and brought the pre amp level up a bit and bam. No more squeals just a nice tone. Now admittedly I lost a little bit of high end but a slight eq adjustment and it seems fine.
Although I’ve noticed a bit more of a noise floor, I need to run the gate harder, but still seems better to me.
Anyone else have similar issues? Or different methods?