In our setup we use various machines and OSs to access our boards via JTAG.
We noticed that running Ubuntu 18.04, kernels 4.15.50-generic or 5.4.0-113-generic does not allow for successful writes of the flash using the lates Linux driver version 2.5.1. After completing the steps erasing the flash and check empty flash completed successfully the write to the flash fails for the first write access (address 0x0) using quartus_pgmw of uqartus version 21.4 and 22.2.
On Windows 7 and Windows 10 the Arrow programmer driver (2.5.21.3) is used successsfully using quartus 21.4 to write to the flash of the board.
The tests have been reproduced on the same machine with the same programmer and the same board running a dual boot setup (Windows 7 and Ubuntu 18.04) to rule out machine specific issues.
This specific machine is a Dell Latitude E6430s Laptop with an intel i5-3340M processor.
The programmer has been baught 1-2 months ago.
In a comparison on the same Linux platform writing to the flash with an intel USB Blaster II is possible.
Also, we are using the default JTAG bit rates (20 MHz for the Arrow programmer) quite often for various tests, e.g. BERTs and eye scans, we think that this is not a signal integrity issue.