N910T acting crazy after root

So after getting my replacement N910T, I rooted it using the method here, and it seemed to go well, but during the process of reinstalling apps, I noticed some erratic behavior like the device not allowing root access when root checker says it is rooted. Or SuperSu not asking for SU access on apps that normally do, thereby denying root access, like Root Explorer. When I go back and check root checker again, sometimes it shows that it has access and other times it says that it doesn't. For a device with a supposedly unlocked bootloader, I've never encountered so many issues. My AT&T S4 which has a locked BL never gave me any issues once it was rooted. With all the devices I've rooted over the years, I've never had this much trouble. So I'm wondering if it's corrupted somehow? Or is there something about this systemless root that is the issue?

Here are the basics:
Android 5.1.1
Baseband OK2
Kernel Version 3.10.40-6209177
Build Number LMY47X.N910TUVU2DOK2

I've read threads until I'm crosseyed and googled but couldn't really come up with anything, so I could use some help here.

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