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A standard OS distribution (e.g. Raspbian) comes with two partitions - VFAT for the firmware, and something else (ext4 for Linux) for the OS itself. NOOBS supports multiple OS's by dividing the card up into slices. NOOBS itself uses 4 partitions, the first of which is a VFAT firmware partition (called RECOVERY), while Raspbian installed under NOOBS is likely to use partitions 5 and 6. When your Pi boots, the firmware in the RECOVERY partition allows you to select an OS then triggers a reboot, leaving just enough information to allow the bootcode.bin to load the correct firmware for the selected OS.
When you put the NOOBS card in a PC it may only recognise the first VFAT partition, and any changes there will not affect the main OS (provided they don't stop the Pi from booting). NOOBS itself allows you to edit the config.txt for each of the OS installations, so that is one solution. Alternatively you can edit /boot/config.txt from within Linux (but keep reading...)
The above explanation doesn't fit the case where you have been editing /boot/config.txt from within Linux and it isn't making any difference. If that is your situation then there is another problem. /etc/fstab lists the filesystems and their mount points, and you should find an entry in there for /boot. For your NOOBS card the mount point for /boot should be /dev/mmcblk0p5, but there was a batch of NOOBS cards made for which that entry ends up saying /dev/mmcblk0p1, which is the partition for NOOBS's own firmware. If this is the case for you, the easiest way to repair this is to update to the latest Raspbian:
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sudo apt-get update sudo apt-get upgrade