“Still present” is related to your previous build for 650D (didn't observed this bug earlier in crop_rec_4k_mlv_snd branch).
May be it has nothing to do with crop_rec. Because this module is not even loaded on my camera.
It seems like mlv_lite itself produces the bug. When 1/25 happens, you may switch raw recording off, turn camera off and turn on again, than it shows real shutter again in 100% of cases, turn raw recording after that and that's ok. Till next reboot, when the luck decides )