Cropping parameters are ignored, or cropping is done but with wrong dimensions
The problem
You merge a video track applying cropping parameters. When you play the file back, the video is either unchanged (no cropping applied at all) or the dimensions are wrong.
Reason
This is a bug in your player. There's unfortunately no easy way around it.
In Matroska, the cropping parameters are stored as four values (top, left, bottom, right) in the track headers. The video track itself is not modified. It's therefore a lossless process.
During playback, it's the player's job to set up video filters properly so that the cropping parameters are honored. The Matroska spec notes page lists the process to use:
PixelXXX (size of the coded image) -> PixelCropXXX (size of the image to keep) -> DisplayXXX (resized cropped image)
You should report this bug to the developers of your player.