Ah I see, #5 is just the header you’re using. You aren’t using 5 total. That makes more sense.
I don’t even have L-connect installed, but I did once upon a time. Maybe I changed a setting there and forgot about it, but I don’t think so. Either way it’s probably worth checking that your bios is set to “PWM” for that header, and that L-connect is set to “enable MB PWM Sync” under the fan/pump profile page. (Just from googling). Look for settings to turn off any L-connect interaction - forcing it to pay attention to the fan header?
I’m wondering if your controller is somehow set to ignore the header pins and run from just the usb port/L-connect. And maybe on a power cycle, your mobo thinks there’s no fan?
I dunno - I’m shooting in the dark now though. All I know is that my controller always shows up as a single fan, and all the attached fans run at the same speed - whatever the header calls for. No software installed, all wired connections are made, exhibits this same behavior regardless of OS, power cycles, reboots, etc.
Sorry I’m not more help - it’s frustrating when things that should “just work” don’t.