Tech support advised using the WebGUI to perform a downgrade to 1.0.6 and then an upgrade back to 1.0.6.1RC3a.

Sadly this also did not update the bootloader or EEPROM version. I even tried flashing and restoring to defaults after each flash. I have contacted support again and explained the situation and will report back what they say.

It's slightly annoying as we just need to work out how to force an upgrade! :p

Sounds Interesting.

I've been having odd issues too, I have had the same DHCP issue from time to time , I have to switch of the power to the unit ( 3900 ) and restart to get DHCP working again.
So far the 3900 is not what I expected, I'm thinking of trying the console now to see if I got bad Flash as you pointed out.

I bought My 3900 for Reliability and Speed however find its the opposite to what i was hoping.

All I run on the 3900 is 2 separate networks (LAN1 on LAN_Port_1 [192.168.1.*/24], LAN2 on LAN_Port_2 [192.168.2.*/24]) with 3 x ADSL Draytek Vigor120's ( 2 x ver.2 , 1 x ver.1 )
LAN2 [192.168.2.*/24] is for Guest Access via untangle server which is also the DHCP as find the 3900 fails on DHCP ( found that giving a MAC on a bind to IP via Drytek 3900 DHCP ended up not seeing gateway / internet and is why LAN2 doesn't have DHCP in the 3900 )

I'm thinking of giving the 3900 a few weeks to sort out if not then might go for a RouterBoard ( RouterOS ) CCR1036-12G-4S

Having similar issues, the 3900 is just not reliable.
I upgraded yesterday evening to 1.0.6.1 and so far the VPN trunk is now down, the 3900 still thinks its up, clicking disconnect doesn't do anything neither does trying to disable the profile. I went to reboot the router, and thought great they have sped up the reboot to be almost instant, until it turned out that the device didn't reboot, the web gui just went through the motions. So now I can't reboot the router without physically switching it off and on.
I find amongst other things the most annoying is:
- when Google Apps Sync sticks on my users machines, only a router reboot will allow Google Apps Sync to send and receive mail.
- VPN trunks go up and down at random and at the moment it seems it has got worse with the firmware upgrade
- Using voip phones with NAT keep alive to maintain the same wan kicks them offline regularly

I could probably presume that the 3900 is causing packet loss and getting itself all confused, then the web interface dies and finally you have to walk into the server room and flip the switch, whilst avoiding a load of users on your back about the internet playing up.

Sounds exactly like my issues , I also had the sudden quick reboot with latest firmware and then 3 hours later noticed dhcp wasn't working so had to stretch into cabinet to switch off the 3900 on the rear .

I'm giving the 3900 a chance to prove itself , how ever manage are having enough with it and want and authorised to replace it with a mikrotik cloud core router ( CCR1036-12G-4S ) as it will also help with hotspot services to take over the untangle server which would mean less electric and more central so less to go wrong

Now that you mentioned google app sync , I couldn't get it to work so had to setup manually in outlook on all machines thought it didn't like windows 7

Draytek ended up replacing my whole unit for a new one under warranty - seems to be working fine right now but time will tell