The Apexi has a weird way of dealing with high electrical load, you have to put it into a config mode that I can't remember the name of and then turn EVERYTHING on and it learns that that is the draw for
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'high'.
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It doesn't have an ELS pin like the stock ECU does.
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Maybe you just need to redo that? Unfortunately that is the sum total of everything I know about PFCs, I don't even know how to get it into that config mode, just that it exists.
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I am also assuming that by
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'apexi ecu' you mean a power FC and not a piggyback.
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Edit:
http://www.paulr33.com/powerfc-faq/powerfc-faq.htm#33