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The X windows keyboard management mechanism (xkb) has a layout option to use one of the keyboard LEDs to indicate which layout is active. If this is enabled in your layout, you could be seeing NumLock on whenever you're in Persion keyboard layout, and off when you switch to English.

To see if this is the case, use the setxkb command, as follows:

$ setxkbmap -query
rules:      evdev
model:      pc105
layout:     us,il
variant:    ,
options:    grp:alt_shift_toggle,grp_led:scroll

This is what I get on _my_ system, which has Hebrew and US-English layouts. Do you notice the grp_led:scroll option? This means that when I'm in Hebrew, my Scroll Lock LED is on. If in your layout you see something like grp_led:num, then my suspicion is correct. You can then use the UI for keyboard layout management to disable this option and use the NumLock LED as it was originally intended.