nope, it will work fine that way. I have all my gates & fkashers hooked up via an IT. You can also power it from a fixed voltage post so it's not depending on track power to active it. (if you are using 2 seperate transformers for this, make sure the ground is common between the 2)
Chris
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Just picked up a mth 262 crossing gate with flasher. Is there any harm hooking it up via an insulated track section? Directions only show using a T. A. D. I know on the scale crossing gates it's not recommended.
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