I recall something about the motec grounding some of the outputs on initial start-up. So if you are low side switching (Sink) a load it will momentarily switch and energise the load on start-up as you describe.
We noticed this on the UWA Motorsport car, which had a small cooling fan that would briefly start and then stop when we switched the ignition on. Basically the relay to switch the fan on was supplied with a fused 12V from the ignition switch and the negative side of the relay was connected to an output on the motec which when grounded would start the fan briefly.
From memory to rectify this you needed to high side switch (Source) the load (which not all the outputs will do) or rewire a relay so that grounding (Sinking) an output will not energise the load.
Bit of a pain.
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