[BrianG]

You can run the cap on any channel that you have free (in your case, maybe only the battery in slot may possibly be open). If they are all filled, run the positive and negative cap wires right in parallel with the fan.

Again, this is a long shot, so don't be surprised that it doesn't help - but it wouldn't be the first time random noise caused problems. This is why I said to run an Rx pack first as a test. If it doesn't work, then you don't have to go through the bother with the cap, although it certainly won't hurt to do it anyway if you're bored.

Usually, when something electronic starts acting up after a while, it is usually related to heat, or constantly running hard.

Something else you could do is carefully cut the shrink wrap off the BEC and inspect solder joints. Cold or poor solder joints could cause things to act up as well since there isn't a solid, low-resistance connection. This is especially important for high speed switching regulators. They need very solid ground paths to prevent feedback to nearby parts and device leads.