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

'high'.

It doesn't have an ELS pin like the stock ECU does.

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.

I am also assuming that by

'apexi ecu' you mean a power FC and not a piggyback.

Edit:
http://www.paulr33.com/powerfc-faq/powerfc-faq.htm#33