Default [Q] [N00b alert] Phone says unrooted when it /is/ rooted

First off, I'd like to say my S2 is the Virgin Mobile version (model i9210) so I'm not sure if it's okay for me to post this in this forum or not. Feel free to move it where it should be, I won't be offended.
Edit: Originally had posted this in the Samsung Galaxy S2 forum, but it was nicely moved to this forum in hopes that it would be seen more~ So to clarify, my phone is the Virgin Mobile Samsung Galaxy S2, running Android 4.1.2, model number SPH-D710.
The ROM I have is BiftorROM-V8-JB-XWLSN-NoWipe.

Onward. This is my first Samsung phone AND my first Galaxy, and when I decided to root my phone, I had no idea how much different it would be from my past phones. How I didn't completely brick this phone, is nothing short of a miracle. I had trouble with some ROMs so someone eventually linked me to a Sprint stock ROM, saying it was compatible with my phone.
Since then I've been using that ROM, despite having a Virgin Mobile phone, with no problem. Recently I noticed an app I use (SD Maid) was listing my phone as unrooted. It was weird but I ignored it, because the app still worked. Even later, I noticed other apps that require root access were not working correctly, so I decided to download a root checker.

Status: Unrooted

Well, then. I'm not sure how this happened, or what's going on, but I figured again, it was no big deal because my ROM was running perfectly and I had no desire to change my ROM or anything else soon. Last night my phone started acting completely different. Lagging like crazy, and when I tried to unlock my phone, it would take a good 15 seconds just for the screen to turn on and my lock screen to start functioning normally. Then another 20 seconds or so for the screen to register my touch and actually unlock my phone. I tried disabling all lockers, but my screen would just turn black and I would still have to wait.

A friend suggested that I simply go through the process of rooting as though my phone really were unrooted and just hope that fixes it, but I'm not sure if that would be a good idea. If my phone wasn't operating so slowly this wouldn't be as big of a problem, but it is, and I'm pretty afraid that I'll mess my phone up somehow.
I once found a forum with the topic the same as mine but I haven't been able to find it since, so I'm hoping someone here could point me in the right direction. Do I go through the root process, maybe try just reflashing my current ROM? I've also thought about just doing a system restore on my phone and see if that helps. Thanks in advance.