mRo X2.1 v2 fails to connect to the bootloader

Hey people.!
I am using an mRo x2.1 v2, running on Windows with cygwin toolchain.
When I try to upload my code (or even any example code - px4_simple_app), it goes into and endless loop when trying to locate the bootloader.

Here’s what I did:

I build the code make auav-x21_default
The console builds it successfully
I try to upload it make auav-x21_default upload
Here is the output :

ninja: Entering directory `/cygdrive/c/PX4/home/Firmware/build/nuttx_auav-x21_default’
[0/1] uploading px4
Loaded firmware for board id: 33,0 size: 1613569 bytes (77.55%), waiting for the bootloader…

Attempting reboot on /dev/ttyS0 with baudrate=57600…
If the board does not respond, check the connection to the Flight Controller

I tried changing a cable, switching a port and the fix mentioned at

Also, I can access the nsh terminal using QGC, but not using PuTTY.