Try the following added to your bootargs:
init=/bin/bash
When the system comes up, remount root read/write:
mount -n -o remount,rw /
cd to /etc/rcS.d
Rename the S18hwclockfirst.sh and S50hwclock.sh to s18hwclockfirst.sh and s50hwclock.sh (lower-case "s").
mount -n -o remount,ro /
sync
sync
sync
Then reboot the system ctrl-amiga-amiga. Boot Linux as usual, and see if that alleviates the problem. If it does, there is probably a bug in the APUS kernel implementation of the hwclock. I use APUS Linux on an A3000D and hwclock works ok, but on CSPPC rather than BlizzPPC. I do not know precisely how the battery-backed clock on BlizzPPC works so maybe this just hasn't been well tested?
Obviously, do the above at your own risk :-)
