OneInchEye: rpicam-jpeg failed to capture "Camera frontend has timed out!"

Camera failed to capture jpeg using rpicam-jpeg --cam 0 -o default.jpg
The issue is related to the camera mode transition between the preview default SRGGB12_CSI2P,2784x1828 to the still pipeline’s SRGGB12_CSI2P,5568x3664/0, for some reason the cmos sensor is not sending a complete frame after the transition that causes the camera frontend to timeout.

A workaround is to ask rpicam-jpeg to use the same mode for preview:
rpicam-jpeg --cam 0 --viewfinder-mode 5568:3664:12:P --mode 5568:3664:12:P -o default.jpg

Using the logic analyzer on the XVS and XHS pin shows that after the transition, hblank is still sending signals but no vblank were asserted. From the pulse measurement it looks like the sensor is stuck at the same hblank interval as the 2.7K state (~4.8us) and hasn’t been updated to the correct hblank of ~10us.

Interestingly no other mode is impacted, only mode 0 (SRGGB12_CSI2P,5568x3664), if we use rpicam-jpeg --cam 0 --mode 5568:3664:10:P -o default.jpg the camera app works just fine, and the hblank duration update can be seen.