first of all, a 'hello' from me as I'm new to the STM-world! Today I sarted with the Cube IDE on Ubuntu and a STM32H743ZI2 NUCLEO board. After troubleshooting the IDE i finally managed to get it working. When debugging, the program is halted upon entry, but every further breakpoint is ignored. Since I tested it on a blinky program, I can tell, that the code is executing. Every other function like stepping seems to work fine. Furthermore, the problem only occurs on my Ubuntu System, the Windwows version works fine.
Are you using the same GDB server on both Ubuntu and Windows? How many breakpoints are you using?
If you're using ST-Link GDB server then please activate the logs in the debug configuration and send it to me and I can take a look at it.