More information is really necessary.  Make and model of battery monitor?  Has it always done this or is this a sudden change? Does is start off at -50 AH and never goes below that or does it start off at different value and then stops at -50 AH?  Do amps start off higher and then taper down to 16 amps?

The AH counter not changing while showing 16 amps is suggestive of something wrong with the meter.  I mean, it's just a counter and it should be counting.  You might try removing and restoring power to your meter or doing a factory reset.  My old Link 20 would occasionally go out to lunch.....

[quote=Talisman]According to my battery monitor it seems I can not fully charge my batteries. My house bank is two Lifeline AGM's of 200 amp hrs each total 400 amp hours it seems no matter how much I motor I cannot get past a negative 50 amp hrs on my meter.  When reaching the 50 negative the meter says its receiving around 16 amps but never goes better than negative 50.  I know resistance increases with charge level but I would think after 3 to 4 hrs of motoring my high voltage Balmar 110 alternator with ARS-5 regulator would charge completely.

Any insights?[/quote]

3-4 hours is nowhere near enough time to fully charge the batteries. Your Lifeline batteries can be considered "full" when they are accepting less than 2A (0.5% of capacity) at absorption voltage/14.4V.. This can take upwards of 7-10+ hours depending upon age and condition. Your battery monitor is also likely incorrectly programmed and your batteries are probably no longer 400 Ah's...  At 16A (you did not say what voltage and this is important) your batteries are still a long way from "full" as defined by Lifeline.....

AMP HOUR COUNTERS 101
Conceptually similar to the electric meter on the side of your house, these devices are supposed to change the counter commensurate to the magnitude of current over time.  If your Ahrs meter indicates -50 at 12pm and for the next full hour your AMP display indicates +16 amps charge, then by 1pm your Ahrs meter should read -34.  The fact that you you observe a static -50 count while the shunt is measuring +16 amps is quite baffling.  Keep in mind that the counter rate-of-change while in ABSORPTION will be much lower than when in BULK.  At 60 amps, your count rate is 1 AH every minute.  At 16 amps, your count rate is about 1 AH every 4 minutes.  So, don't be mislead by the nonlinearity of the count rate.

BATTERY RECHARGE TIMES
If you've taken 200AH out of your 400AH battery bank you'll be in BULK phase for maybe 2 hours, restoring about 100AH, leaving your bank at 75% charged.  The remaining 100AH will be primarily restored by the ABSORPTION phase which could be another 6 to 8 hours.  The display on your ARS-5 will tell you what charge phase you're in, but fair to note that +16 amps is quite typical for ABSORPTION current on a 75% depleted 400AH bank.  Bigger alternators certainly moderate BULK time, but really have no impact on ABSORPTION time, which is typically 80% of the overall recharge time.

ALTERNATIVE
We keep Whimsea on the hook and use her as our weekend home, regularly drawing 200AH over the weekend with minimal engine run time -- usually just enough to get out of BULK.  To complete the charging, we have a 100W flexible panel on the dodger.  During a typical week, the remaining 100AH ABSORPTION deficient is fully restored.  The panel + controller was about $250.

Like most flexible PV panels, ours has grommets along the edges.  Currently, our single PV panel is simply "laced" onto the corners to the dodger frame, but a more elegant install would be basted Velcro patches into the top of the dodger cover and adhesive-backed Velcro affixed to the underside of the PV panels.

The PV wires (with MC4 connectors) are led down the aft-cabin hatch, across the edge of the bulkhead, and then through the bulkhead above the breaker panel.  This is where the PV controller is mounted so the status lights are visible.  From here, the battery cables are routed down the edge of the bulkhead and into the breaker panel area to a "hot fuse bank" (bilge pump, battery monitor, stereo memory, and solar controller).  Even with the PV wires, the small hatch can be dogged down to the partial position and since the hatch is protected by the dodger, no water gets in.

I wish I could help with your issue. I have a Blue Sea Ahr counter.
Have you checked out Main Sail's site? He has 2 good articles on the AH meters and one on a new Smart
SOC meter made by Balmar. This new State of charge meter is on my Xmas list. I do get tried of guessing on what my battery bank's SOC really is.
Main Sail has a ton of good info on a lot of stuff.
It's a really good read.
http://www.pbase.com/mainecruising/smart_gauge
http://www.pbase.com/mainecruising/programming_a_battery_monitor

Enrique,

For the first 90 minutes the math was OK.  When you go into FLOAT, the LINK 2000 will reset Ahrs after a certain amount of time and start counting up.  All seems to be working as designed.  But you might want to fully charge your batteries, reset on your LINK 2000, and re-input your battery parameters.

Enrique,

You need to understand more about your Link 2000 and how it works.  I have a Link 2000 which controls our Freedom 15 I/C pretty much identical to your installation.

For everyone installing a battery monitor:  The "Gotcha Algorithm" thread, a "MUST READ"

http://c34.org/bbs/index.php/topic,4922.0.html

DEFAULTS are factory settings that are made to be modified to suit your setup.

There's also this:  http://www.pbase.com/mainecruising/programming_a_battery_monitor  I just noticd it was previously provided.  Good stuff.

Also, you need to understand battery acceptance, as they get fuller they accept less charge.

The Link 2000 also shows battery voltage as well as NET amperage of your system.  You don't have to only look at the regulator.

Here's where I mounted my solor controller.  The shelf above the nav station in the aft corner.  The wires are routed behind controller and then behind the long trim board.  The PV wires go through the bulkhead, to the aft cabin, and then up through the opening hatch.  The battery cables go down from the controller into the back of the electrical panel to a "hot" fuse block.

(The solar controller is mounted upside down in order to help keep the wires from being disturbed by objects on the shelf).