You're obsessed! Look, you're charging/discharging batteries for Gawds sake, not measuring the velocity of a speeding bullet!

Who cares if it's exactly an hour, or an hour and 15 seconds...

Do your ADC's, do your calculations (assuming a 100mS time interval), insert a Pause 100 and simply Loop. Just forget the time for the ADC's to operate and your math time. Just do a Pause 100.

The first time you run your program insert a message to appear on your LCD after 36000 loops... (an hours worth of 100mS loops). You run a stop-watch and compare your watch against the PIC. You'll probably find it'll be an hour and a few minutes. Calculate the overspill time and reduce the Pause 100 statement accordingly. Hey presto - you're done.

Now, if it ends up a few seconds out per hour, the batteries aren't going to care, after all they're a big chemical pile and you can't predict how chemicals will react from charge to charge, let alone down to fractions of a second. You're going to charge a 2200mAH Battery for example... it'll behave differently when factory fresh to when it's a year old. Best guess is close enough. So if you're charging a Battery for an hour, so what if you charge for one hour, one minute and seventeen seconds? It's not going to hurt.