Hi there,
I recently had a similar issue to this, I don't use Kernel care (Although did consider it at the time and tested on a separate machine) the problem is usually that there is a kernel update that was downloaded by your server. with kernel care, it seems to be if you have installed kernel care after the new kernel is downloaded - but not activated, this means kernel care patches your current kernel while the new one remains untouched - reinstalling cPanel won't change this as the Kernel is generally updated by YUM and is not a WHM process. So while it is safe for kernel care to patch your "old" kernel. You will still have the new one in the list and your server will still think its the latest and most up to date one.
Kernel care would then patch your current loaded kernel - this means that your server / WHM will still detect the newer kernel in the kernel list and basically wants to use it. Even though your "old" kernel is fully patched by kernel care
Generally what you need to do is to edit your grub conf and select your current loaded kernel as the boot kernel. This should then remove the message as WHM and your server won't detect a kernel version mismatch.
In my case, my kernel updated and I rebooted (without kernel care) the new kernel crashed the system and stuck my Dedicated server into its emergency mode. Tech guy at the DC booted to the previous kernel for me and I then had to update the grub conf to the previous kernel HOWEVER, After a reboot (I wanted to test that it was sorted) the reboot message reappeared, I noticed that the Kernel that was booted had changed its ID number, I had set it as 2 as the rescue/emergency mode was 0. This meant after the reboot, 0 became the "new" kernel which doesn't work and 1 became my stable one. So I had to change the grub conf again to book kernel ID 1. Basically, the server did boot the correct kernel but that same kernels Id the changed from 2 to 1 (I'm assuming after a succesfull reboot).
Anyway I hope this helps shed light for those experiencing this issue.
The following commands can be used to find and set the correct kernel, on the last one change '1' to your desired kernel from the awk command
# awk -F\' '$1=="menuentry " {print i++ " : " $2}' /etc/grub2.cfg
# uname -r
# grub2-editenv list
# grub2-set-default 1
this article explains deeper
HowTos/Grub2 - CentOS Wiki
