I can probably guess, but are you saying that you removed the actual guide button (from the turbo PCB), or that you disabled/removed the whole turbo PCB? In either case, the first thing I would suggest is to plug the stick into a PC, after making sure the PC has the Xbox for Windows drivers installed. If the guide window still pops up, you know for sure the problem is in the stick and not the game console. Yes, it’s unlikely to be the 360’s fault, but it could save you a lot of time if you confirm it. Next, I would go over the PCB(s) with a magnifying glass and see if there’s any metallic debris that could be shorting something out. Pay special attention to the contact pads or legs of the ICs. If you don’t find anything there, check the ribbon cables for visible damage.
If everything seems OK but the problem persists, there’s one last thing you can try, and that is to unplug one of the ribbon cables going from the turbo PCB to the main PCB. Maybe check Toodles’ Kitty install guide for info on how to do this safely, as the connectors have glue on them to prevent them coming loose. The cable in question has a wire marked (on the main PCB) as ‘XGUILD’. Once this is disconnected, if the Guide is still coming up then it is almost definitely the main PCB causing it. It could also be the USB cable shorting, but because all data is transmitted over one single wire you would probably be having far more severe symptoms.