blietzkrieg - it sounds like you've checked the basics in terms of software configuration, so it's probably something wrong with the hardware.
Since you seem to have several things not working, I'd focus on one thing at a time. In this case, one output port at a time. Take one output port that's not working and focus on figuring out why. Ignore the others for now. Once you figure out that one port, move on to the next non-working port.
I'd start with one of the non-working flasher ports. Some of those seem to be working correctly, so you can rule out a number of things, such as a bad data connection to the TLC5940 chips on the main board, completely dead TLC5940 chips, or bad power connections.
One question first, though: for the flasher ports that are working, are they working reliably and consistently? If you go into the config tool and bring up the output tester dialog, do the working ports all respond properly when you slide the brightness slider across the range? Do they all turn both on and off when you tell them to? Do you ever see the wrong port being affected when you're changing the brightness on any of the flasher ports?
The reason I ask is that I want to make sure that the working ports are all responding to commands, and not just stuck in the "on" position or responding randomly.
If you're satisfied that the working flasher ports are all working correctly and reliably, that narrows things down quite a lot for the non-working ports. The problem then has to be in the components between the TLC5940 and the flasher output. There are only two components in that section: the PC847 optocoupler chip, and the UL2064BN chip.
There are two main troubleshooting techniques once you've narrowed things down to that level. The first is to get out the schematics and trace the connections from pin to pin on the affected circuit with a continuity tester. One common problem is a bad solder joint at a pin connection (between a pin and the circuit board). Those can be difficult or impossible to spot visually, so a continuity test with a multimeter is the best bet to find those.
By the way, as a general troubleshooting tip, it's extremely helpful to look at the schematics and board layouts live in Eagle. There's a free version of Eagle that you can download from the manufacturer's site:
https://www.autodesk...e/free-download
Once you have that, grab the schematic and board layout files (.sch and .brd) from my site and open them in Eagle. On the board layout, you can right-click on any IC pin and select SHOW from the right-click menu to highlight the circuit traces that connect to that pin - that shows you exactly where that pin should connect electrically, which makes it really easy to find the right points to test with your continuity tester.
For example, let's look at how you trace flasher 1R (first flasher Red). On the board diagram, find that pin on JP11. Right click it and select SHOW. That lights up the trace to IC5 pin 2. So you'd test continuity between JP11 1R and IC5 pin 2. That's the Darlington output that drives the port. If that looks good, we move on to the input side to that Darlington. You can figure out the Darlington input/output pairings by looking at the schematic. We go to the schematic for IC5 pin 2, and you see that's labeled "O1", meaning "output 1". The corresponding Darlington input is "I1", input 1, which is pin 3 on the same chip. So we right-click IC5 pin 3 and select SHOW. That lights up the trace from IC5 pin 3 to OK1 pin 15, so that's the next trace to test with the continuity tester. If that looks good, the next stage is the input to that optocoupler. For the optos, the pin with the little arrow pointing outwards on the schematic is the output, and the pin opposite on the schematic is the input - that's the pin on the "bar" side of the internal opto LED on the schematic diagram. So in this case, OK1 pin 2. So repeat the process there: right click OK1 pin 2. That gives us a trace to KC2 pin 28, so continuity-test that.
If all of those look good, there are some more continuity tests you can make. Go back to OK1 and test the other pins that connect to the same square on the schematic - namely pins 1 and 16. Those are the power connections, so when you SHOW them in Eagle, you'll get a huge network of traces light up, as lots of things need power connections. For all power/ground connections like this, the only thing you have to test for continuity is the connection all the way back to the main power connector pin. If that's good, this particular chip is getting power, and that's all we care about at the moment.
If the connections all look good, it's most likely a bad component. Again, there are really only the two components in this particular path - the Darlington chip and the optocoupler chip.
If your chips are socketed, the easiest test is always to swap chips. Of the same kind, obviously. All of the UL2064B chips are interchangeable, so you can swap, say, IC5 and IC6. Likewise, the PC847 chips can all be swapped around, and the TLC5940 chips can be swapped. Swapping chips is an especially good test when you know that one chip is working. In your case it would be harder to interpret the results given that it sounds like most ports aren't working properly, but it might still provide some useful information: if the exact set of working ports changes when you swap chips, it's likely that the problem is with at least one of the swapped chips.
As with all debugging, do one thing at a time with the chip swaps. That is, swap a single pair of chips, and test to see what happens. Doing multiple swaps at once will confuse matters because it will make it more difficult to tell which swap had which effect.
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