What do you mean by the volt meter not showing charge? What is the range of the meter?
Some pics required
Printable View
Is this a blue $99 Jaycar dual battery controller by any chance?
Regardless if it is or isn't, your second battery will only start to be charged once the main one reaches a certain voltage, say after half an hour. I'm not a battery wiz but I'm under the impression it is impossible to charge a battery to 100%.
DL
My question is " How flat is the second battery?"
It is quite normal for a second (AGM 90AH) battery to charge at say 13.4-6 volts when reasonably flat even in my case with a dedicated 85amp alternator. This increases slowly to say 13.8-9 which is about when the battery is 90% charged. Full charge may take another couple of hours in my case when the charge rate is reading 14.1-2 on a 30c day.
With a 60 amp alternator and aircon running there is not much left over for the second battery and these times may elongate to 4 hours or so to reach 90% and may longer than a day's driving for 100% or 14.1 volt charge rate.
I found this situation when in NT and my second alternator died and I bridged to my main 85 amp. It took more than a day for the combined charge rate to reach 14.1 with the main battery effectively starting at 12.4 or so and the second at 11.6-8. No isolator fitted.
So your situation sound pretty normal with a 60amp alternator if the second battery has say run a fridge overnight. It will probably rarely get to 100% charge.
Regards Philip A