Update:
At the recommendation of some, we installed Wireshark to capture/analyze the network traffic between our Watchout cluster and our PJ-Link projectors. We found that the failure to send commands occurs when those commands are attempted around the time that the Watchout/PJ-Link connection is severed (seems to be a 3-10 second window). For clarification, here is an example of a successful attempt, followed by a failed attempt...
Success:
Shutter Close command sent
Wait either less than 50 seconds, or more than 1 minute 10 seconds
Shutter Open command sent
Failure:
Shutter Close command sent
Wait between 50 seconds and 1 minute 10 seconds
Shutter Open command failed
The above is a general approximation, but based on those times, we were able to determine when to expect those commands to fail. On another note, we have tried the same concept with a Panasonic PT-EX600 (with internal PJLink protocol), and it closes its connection after only 30 seconds.
Currently, our solution to either case is to loop an auxiliary timeline with an empty carriage return to each projector. Our loop runs about every 15 seconds. This seems to keep all connections (including our Panasonic projector) open instead of risking that a command be sent during the previously mentioned time. We feel this is currently our best option, though perhaps there is something we haven't thought of. If there is anyone that sees any potential issues with this (or as always, if there are any questions), please let us know.
Thank you.