I suspect its the custom kernel.. but you could try to troubleshoot by pulling a logcat from the phone, and see what exactly is the cause.
fair warning.. deciphering the logcat can be difficult.
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Current: OnePlus One CyanogenMod 11 M9 and Galaxy Tab 2 10.1; SlimKat
Past: Galaxy S5 XtreStoLite
Galaxy S4; Samy Deluxe Jelly Biafra
Nexus 4; Z1 ROM (xperia XL)
Galaxy S3; SlimKat
Galaxy S2; HellKat (Diablo kernel)