This seems strange. Not (yet) having a lot of experience with Solus, maybe a specialist needs to look at this. What I have found is:
- clr-boot-manager modifies /boot/loader/loader.conf
- setting a timeout this file contains a line
timeout x (with x being the timeout)
- when no timeout is set, this line is not present
Maybe you can just mount your EFI partition to
/boot and check if the contents of
loader.conf are modified. If this is the case and still not working, I have no clue.
Just to be sure, you are using UEFI mode, not grub, right?
clr-boot-manager set-timeout will write the value to
/etc/kernel/timeout. This file just contains the integer value. Thus, you could try to see what happens if you just remove this file and then do a
sudo clr-boot-manager update.