I've seen this on a RB433AH box too with 4.4. I removed a secondary default route, rebooted, and it showed up again.
I did notice that while deleting one of the static routes, the delete command (via SSH cli) hung for a bit before completing, and on another 4.4 RB411 (or was it a 433?) box, a static route removal timed out completely.
So I wonder if perhaps this is related.
Here's my latest attempt at old default route removal:
[admin@RB433AH] > /ip route print
Flags: X - disabled, A - active, D - dynamic, C - connect, S - static, r - rip, b - bgp, o - ospf, m - mme,
B - blackhole, U - unreachable, P - prohibit
# DST-ADDRESS PREF-SRC GATEWAY DISTANCE
0 A S 0.0.0.0/0 10.20.30.41 10.20.30.40 1
1 S 0.0.0.0/0 10.20.30.41 10.20.30.1 2
2 S 0.0.0.0/0 10.50.60.22 10.50.60.1 2
[admin@RB433AH] /ip route> /ip route remove 2
action timed out - try again, if error continues contact MikroTik support and send a supout file (13)
[admin@RB433AH] > /system resource print
cpu: "MIPS 24K V7.4"
[admin@RB433AH] > /system routerboard print
In the case of the old default route I was removing above, the 10.50.60.0/24 network and IP address had already been removed from the MikroTik. I don't know if that is relevant or not.
Also, AFTER the command times out, doing another "/ip route print" will NOT show the removed route. It appears to be deleted, although it will reappear again after reboot.
When others have encountered this problem, did any of you have the command time-out?