Sorry if this was asked already, but does the same USB work with usbloaders (not in neek)?
It could just be an incompatible drive. If u have done everything the same on a different drive that works, and u still want to try to troubleshoot this, I would try different versions of neek2o. If that still doesn't work, I would disable Modmii's neek2o option and build the original neek, and if that doesn't work I'd try older versions of that too.
The only other thing I can think of is if the drive isn't getting enough power or it's very slow to initialize. But if u can load the HDD from GX and launch uneek from within the app then it should already be initialized. So if u try that we can rule that out too.
Nah his syscheck looks fine (perhaps a bit cluttered, but fine). That wouldn't be causing this issue.