The first line of text clover shows just before the clover GUI loads shows 3065
Both Clover Configurator and the Clover System Preferences pane also shows 3065
I use the packages downloaded from clover to do the updates.
The problem is, that your fusion drive is seen as two or more independent partitions on different disks. Now, when you boot UEFI mode, you run Clover from one or the other (depends on your mobo/clover logic/etc) EFI partitions (you have one for each GUID-formatted drive in the system). The problem here is that clover updater cannot figure out where to update its UEFI components/drivers - it knows where it booted off from, but it is not guaranteed that the next time it will root from the same ESP.
Now, here's what I do to update my Clover:
=== DO THE COMMON SENSE CHECK - ENSURE YOU HAVE BACKUPS, BOOTABLE DRIVE TO REINSTALL THE SYSTEM, ETC. JUST IN CASE SOMETHING GOES WRONG ===
1) format a USB flash drive/SD-Card/external drive (any size, even 1Gb is ok) in GUID mode.
2.1) run the Clover installer/updater and install it to the USB to update the Clover EFI modules on the USB
2.2) run the update on the target system (Macintosh HD) to update stuff in /Library etc..
3.) copy updated CLOVER.EFI and others from the USB's ESP to that of your boot drive (that is most probably disк0s1 - you should know that better). Preserve your config, kexts, and whatever you know should not be overwritten.