I don't run any dirt pedals in front of my HXFX. Just the HXFX and the amp. Wired in 4CM. The FX loop raises the noise floor so if there's anything with moderate to high gain in the HX's loop, it will pick up the added noise and amplify it.I think the noise issue that happened early on with the HX Effects has to do with the main inputs, not effects loops. Depending on the type of pedal (or amp preamp) in the loop, noise can be an issue. The effects loops themselves raise the noise floor a little bit. With clean stuff, you don’t really hear it because it’s still low. With high gain stuff, the noise floor gets elevated to the point you hear it as white noise. So if you’re running a high gain amp in the 4CM and put a gain pedal in front of it, that can be quite noisy. This is a white noise, hiss sort of noise, different from typical ground loop noise, which is more like 60Hz hum/buzz.
I wonder why they don't add a noise gate as an effect. The GE300 Lite I just got has a noise gate, actually three of them, and they all work very well.