Recently (the past few weeks), the in-built unread SMS notifications function has been correctly detecting new unread SMS messages, but has not been detecting when they have been read. Thus, it simply increments the number indefinitely.
I have found a temporary solution by changing the formula from the default from $uc(sms)$ to $ni(pcount, com.google.android.apps.messaging)$.
Hi Jordan, this is super strange, Kustom reads directly from the underlying SMS database so this shouldnt be happening at all, does a reboot fix?
Just as a reference a similar question has been posted recently on G+ community and this was referenced in the answer as a solution https://plus.google.com/107597892325032860781/posts/GaTMr2tcqvg
Closing this as it seams an Android Messenger bug, there is also an app on the store that is expressly meant to fix this and its available here:
https://play.google.com/store/apps/details?id=net.tsoft.resetunreadsms
this is not solved. the app just resets it to zero, it stays at zero no matter how many texts you get.