Hi edarmg,
Speaking from experience, it’s possible that you are running in bandwidth issues on the JTX1 and it is very likely that your desktop’s IO bandwidth is much greater.
If you really must save point clouds, then instead you should only save the depth and RGB images (and necessary information like the camera’s intrinsic and extrinsic parameters), and then convert these to point clouds, say on your desktop, or in a less bandwidth demanding process on your JTX1.
ROS (robotics operating sytem) proved very useful when I did this: among a lot of other stuff, it provides tools for logging and converting depth maps to point clouds.
I hope this helps.
Cheers
Galto