You said one of the boxes took 'hours' to upgrade do both boxes appear to work OK, can you pause live TV on both boxes or rewind the live TV you have been watching, this would give the hard drive's a quick check. Can you set programs to record on both boxes.
The recordings you get the error code with is the error code on both boxes, or just when you stream the recording from box to box. You can check your network connections if you press Home, Settings, Network, Diagnostics. You should have, Signal Quality Good, and 3 green ticks.
Are both boxes set to fast start or active start, and have you tried rebooting the boxes by turning the power off and on with either the switch on the back of the box or at the plug.
You could also try a factory reset of the boxes.
It's only a partial system reset and not a complete factory reset.
You are given 2 options,
Choose Keep Recordings, that means you won't lose your recordings and any planned recordings or series links you've set up, you will have to sign into your apps such as iPlayer, Prime, Netflix and ITVX again, also Match frame rate and Standby power consumption will go back to their default settings if you have changed them.
If you do have a faulty box the factory reset might make it fail, if it does you can either call Virgin on 150 from a Virgin phone, mobile or landline, or 0345 454 1111 from any other phone to report a fault, or wait here for one of the forum team to pick this up which might be 2 to 3 day's.
When phoning choose the option to report a fault, then ignore all the options offered and you should then be placed into a queue to speak to someone.