Hello, @kabraham_abin
Indeed it looks like a bug on our side, so I have been investigated this issue and I fixed the problem.
As a quick workaround, I am going to attach a zip where you will find 2 files. You just have to copy these 2 files into the following directory: {toolbox_path}\NXP_MBDToolbox_IMXRT1xxx\mbdtbx_imxrt\+mbd_imxrt\+reg
It should work and you should see the PWM registers inside the registers blocks.
Let me know if this works.
Regards,
Stefan.