Thanks for both your inputs, I am going to experiment using dry sweeteners although I did really want honey to work out, I just can't afford to have half my batches not turn out well. I will calibrate the temperature on the machine as well.  My last batch I lowered the room temperature and it turned out great so that may be a huge issue.  I always run a dehumidifier in the room on days I make chocolate but I live in a humid climate so even with the dehumidifier running all day it still is usually 50-55% RH.  I use dehumidifying packs in the fridge as well. They are rated to dehumidify a small room so are ample enough for the fridge.  It's the same as those little packs you get in some products except I got large canisters of them that are reusable by drying in an oven.

Keeping a notebook is a great idea, I may try that. Thanks for all your tips.  I'm going to experiment on a few of those and see how it goes.

A couple of other ideas. 

Using honey in a Chocovision machine may reduce the amount of mixing getting done. If the CB crystals are not distributed evenly then streaks on the front or back will be common. Break a bar at a streak to see if there is a difference in temper in the cross-section. If there is it is probably insufficient mixing, at least in part.

Also - you're working in small batches and even minute changes to the recipe and ambient humidity will affect the rheology of the chocolate, which will affect temper. You need to assess the temper for every batch, not rely on the machine to do it for you, or rely on a specific set of temperatures. This is a common problem that people who make chocolate fail to take into account. The recipe might be "the same" but small differences in processing and mixing can make a difference in the working characteristics of a chocolate.

Calibrating thermometers is important, but it's also important to know what the temp and RH are in the immediate vicinity of the tempering machine. Keep a notebook and when things don't go as planned, you might find that temps and/or humidity are part of the issue.

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@DiscoverChoc

Off the bat, I can say that honey may cause issues. Honey contains water, and water and chocolate dont mix. It can cause the chocolate to seize and pull the cocoa solids out of suspension. However, whatever your doing you're getting to the point where you can pour into molds.  The issue looks similar to what I've been fighting all chocolate season. No matter how I temper, the molds wont set right and they fall out of temper.

Two things that solved the issue for me is a) double check your thermometer and calibrate your tempering machine. It may not be working right as the thermistor may have drifted somewhat and if possible you may need to recalibrate that, or work around what the drift is. Part of my issue is my thermometer was off by over 4F, so when I was tempering I thought I was "within range" but in fact, I was 4F hotter than the upper limits of the range, so I was never actually in temper to begin with.  That may or may not be your issue here, but after 2 consecutive years having similar issues it's my first go-to troubleshooting step when tempering is an issue.

Second is the temp your molds are setting up/cooling in.  If that's too warm, the chocolate can fall out of temper.  From trial and error experience as well as reading a bit online, optimum room temp to deal with chocolate is between 68-70F/20-21C  It may be beneficial to get a cooling tunnel, cold box, or some sort of cooling area for the chocolate.  Optimum temps based on various forum posts seem to be 55F/12.8C, I'm still working on my cold box which is a temperature controlled fridge setup with a fan inside for airflow.  55 is my starting temp.

You have a chance of running into issues using a fridge, although it is quite possible and many do that without issue.  The problem is a refrigerator will end up by being too cold. And as a result if you leave the molds in too long, condensation is a very real risk. If condensation forms it can cause sugar bloom and ruin the batch. 

Something else to note that you didnt mention: Are you performing a temper test to ensure the tempering machine is giving you proper temper or are you relying on the machine to give you tempered chocolate?  The reason I ask is you can see my results. My room temp rose up to 74F/23.3C. Which, frankly, is normal for my area.  However, I'd get a clean temper test, but the molds would start to swirl and/or discolor.  The back swirls are obvious, the discoloration of the chocolate touching the molds wasnt any different in most respects than what you've shown.

updated by @timwilde: 02/16/16 02:39:46

A certain percentage of each batch I make turns out like the picture below.  I am not sure what is going on and some batches are worse than others and some are way worse than whats shown in the pic. I use the revolation chocolate tempering machine doing approximately 20 pound batches. The settings are 89 degrees temper point and 6.5 temper delta. I recently changed to these settings as before I was using the default settings on the machine for dark chocolate. It didn't make a difference though. I use polycarbonate molds and I have found that the best way to minimize this problem is to set the chocolate for 30-40 min at room temperature and then give them about 15 min in the fridge.  I tried setting them only at room temperature and that seems to make it worse and I have tried setting straight in the fridge without the room temperature time and that also makes it worse.

I read that it is good to warm the molds before pouring chocolate into them so I tried that and it seemed to make it worse. I do find that the first pour into the molds always works the best but I only have enough molds to do half the batch at a time so must do subsequent batches. I have tried wiping the molds with cotton wipes between pours but that didn't help. It definitely works better after my molds have been cleaned with water and dried properly but that takes a long time to do it between every pour and I generally only do it at the end of the batches. Any suggestions on better ways to clean them between batches?

I use honey as a sweetener so would that have anything to do with it? The bars are around 60% cacao paste, 10% cacao butter and the honey makes up about 20% with the remainder being flavorings. I have a 90% bar that is 90% cacao and only 10% honey and it tends to happen less in that flavor but still happens sometimes. The picture is actually from a batch of 90%.

Please help!