Website Pixel nullifying Shopify (and Google Analytics)

[jem_digital]

Hey there! 

I have built several Shopify sites in the past, as well as worked on many more, but never have I seen this one. 
I need to add a custom pixel onto a few pages on the website, these are not Facebook pixels but rather display ad tracking pixels. 

Each time the code is added to the header section of the website, it nulls the Shopify Analytics and Google Analytics too - basically we know there is traffic going to the site, but when the pixel is live, all analytics is at 0. 

Has anyone come across this before? Does anyone have any suggestions as to approaching this? Aware without Shopify Plus we can't add tracking pixels to checkout, but I am just talking about homepage and collections pages. 

Cheers