Intermittent remote unlocking problem - Why 3 mins before it works?

Hi guys, here's one to test you.

- My UK Honda CRV 2008 2.2 Diesel started having intermittent remote unlocking problems
- On first press of key fob, nothing happens. If I wait 3 mins (2 min 45 secs to be precise), doors unlock and alarm disables, and I can drive the car
- If I open door manually with key the alarm will go off and I have to wait the same 3 mins before I can disable using the key fob. So, car HAS to be opened with key fob.
- Cannot start car while alarm is sounding as immobiliser kicks in (green key flashing)
- Changed fob batteries, and tried both fobs, but same symptoms
- Started happening in mornings only, then ok rest of day, but now happening throughout the day at random
- "appears" to be happening more often when colder, but cannot show this conclusively
- Had car battery checked (load tested) at several garages, including at Honda, and they all said car battery good but showing it needs a recharge (73% charged). (Indicator on battery also shows green for good)
- Charged battery up on car, (showed 12.3v initially) but still intermittent issues persist
- Even charged up fully, drove to local auto electrician and had bettery tested good and 100% charged, but then the issue occurred while chatting to electrician within 5 mins of battery testing ok!
- Electrician confirmed remote key fob working and sending signal so issue seems to be with receiving and decoding the signal?
- Even tried the on-line guides for reprogramming the Honda key fobs
- Never had an issue with starting, ie cranking so didn't suspect car battery

Any ideas what this could be? It is driving me crazy. Worst of all, the weather is getting bad now and when I return to my car while out and about in the dark and rain, I have to stand there for 3 mins looking very suspicious before I can get in and drive off!

Could the main car battery be bad somehow, or is it an electrical issue, eg ECU / Immobilser / Transponder / Relay type issue?
Main dealer says it has not heard of this before and will take some diagnostics to pinpoint, but as it is intermittent, it may not happen while they have it so may run up costs.

The main thing I can't find anywhere is **** WHY 3 MINS BEFORE I CAN UNLOCK CAR? *****

Any pointers would be appreciated.