Responses/comments to your questions:
1. What does the yellow/amber light on the protocol adaptor light mean?
these are the link/activity leds for the ethernet connection.
2. I have note yet physically inspected the protocol adaptor per ogdento's post above, but I read elsewhere and noticed in the photo there is a battery inside the unit. What is the battery for and could a dead battery be causing this behavior? I am just surprised that there is a battery inside a sealed unit.
the battery is to keep the clock running on the lower "Rabbit" board when the power goes out. i can't imagine a dead battery causing the behavior you're seeing, it should only ever be used when the power is out to the PA - but you could check it with a multimeter and see if it's over 3volts.
3. Crazy as it sounds, I read another post about a couple people solving problems by turning the protocol adaptor upside down. Any any truth to this? The only thing I could imagine is perhaps improving the connection with the battery if the battery is critical.
i could imagine a situation where flipping it over COULD make it work... but only if it "cured" a loose connection on the ethernet cable and/or rs485 (black/green/yellow/red) line. anything else feels like a stretch
4. If I rule out the protocol adaptor and need a new control board what is correct current model number? I currently have a Compool Easy Touch Upgrade, model 521103. This replaced the original Compool LX3800. It seems like Pentair no longer makes my upgrade model 521103. However, I found another Compool Easy Touch Upgrade model 521107 (without transformer) and 521247 (with transformer kit) and it seems compatible, but a) how do I confirm that it is one of these two, and b) what dictates buying it with or without the transformer?
i don't know what the compool part numbers are but since you do have working communications - albeit intermittent - I doubt the outdoor board is the problem.
your system's communications can of course go in and out intermittently, but the comm port on the board doesn't "work" and then "not work"... if the port - and I'm talking about the physical chip that drives the rs485 bus - on the board is broken, then it's dead and it will never work again. any "intermittent" communications behavior is almost always a problem with the wiring. it can be another device on the system but you'd see an issue whenever the problematic device is powered up and connected - as you did with your old is10 spa-side remote... one caveat being i'm not completely sure if the PA could somehow introduce some intermittent comm issue (you referenced another post regarding it, but that was news to me although I'm not intimately familiar with the unit)
As a test, hook up your devices to your outdoor board with short lengths of "known-good" cable... see if everything works. you likely won't be able to do this with your pump of course, but you can hook up the screenlogic PA and your indoor panel this way.
If you want to try an alternative to the screenlogic, check out the node js Pool Controller on this forum. it's incredible stuff, and runs on a raspberry pi or almost any computer you've got available.
Oh, and if you're re-doing your comm port connections, get your connectors at digikey or mouser... don't pay more than $4 each for them (ignoring shipping). this is the part:
Riacon 4 PIN, Metz Connect, 31007104