The problem with inline fans is that they are designed to transport air from one place to another through a smooth duct not to create high suction at an opening. These fans work better at removing exhaust for lampworking when they are hooked up to a large overhead exhaust hood where the fumes can naturally rise up and be forced into the exhaust tube by the shape of the hood. The length of the exhaust tube and the position of the fan, as well as the fact that the tube is corrugated vs. smooth all have impacts on the amount of air you're actually moving. If the free rating of the fan is around 400 CFM, I would guess that you're getting something around 250 CFM once it's hooked up.
Because the fan is far from the funnel opening there's likely to be very little suction at the opening of the funnel, and what suction there is drops off very quickly to nothing as you move away from the face of the funnel. So for the fumes to go through the exhaust tube they have be pushed in by the force of the torch flame. Heat and exhaust products are rising up in column from the top of the entire flame, not just the tip, and those probably don't get captured by your exhaust. Also when mandrels and glass rods are placed in the flame they cause turbulence so the fumes are scattered around and mixed with air that rises up and fills the room polluting your breathing air.
Assuming there's enough makeup air and that the makeup air source isn't being polluted by the exhaust, either using an overhead exhaust hood or placing another exhaust fan up higher toward the ceiling could help.
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