I am sorry to hear you have some problems while programming the board with Windows. I would like to ask you some questions to identify the root of the issue and solve it.
1. Are you using the Quark D2000 microcontroller development kit?
2. Did you update the ROM first?
3. Could you add some screenshots of the error messages you get on Eclipse?
4. I’m not sure if you have already seem the Limitations and Know Issues in the Intel System Studio 2016; as you can see in there, if you use the UART-B or PWM0 signals, this may produce some problems while uploading code.
5. If you are using the Quark D2000 microcontroller development kit, in the schematic you can see that the FT232H uses its own crystal.
Please let us know as much you can, so we could replicate your environment if possible.
I am running the processor in our own hardware. The Jtag interface I use is a copy of what is on the dev kit. If I use the ISSM Update Rom on the Eclipse platform that works fine every time.
I have built my own code for the OTP rom area as the delivered code tries to switch to crystal osc.
That seems to work. The code executes to 0x180?054 in the flash where I have an endless loop. Trouble is if I change the code and go back to debugger it does not reflash the part. No errors. It just debugs with old code loaded. I took the other projects out of the work space and reloaded eclipse etc.
As regard 4 i am aware of the potential to brick the device but I think if that had hapenned the debugger would not be working at all. Debugging and prog OTP rom are fine. I just cant find what stimultes Eclipse to try to program Flash.