First, don't forget that you should register the ID here if you plan to share them to avoid conflicts (although, to be fair, with a prefix that long, it's certainly unlikely haha).
The conflict is because when a decks is created, its land pool uses a similar ID, but with '1' between the prefix and the deck id (as seen in the 3rd green box). So, in order to use the 3 digit method, you'd need to re-export all of the ones you've already made using only 2 digits. Otherwise, your first hundred 3 digit decks' land pools will all conflict with your 2 digit decks' main deck files. (And after that, the next 2 hundred will conflict with regular unlocks and promo unlocks if there are any.)
That's probably what's causing the issue. The game sees two decks (the deck you're trying to load and the conflicting land pool) with the same ID and tries to load some convoluted combination of the two or just can't understand how to properly keep track of which deck files belong together, resulting in strange behavior.
Sorry, but I forgot about this when I suggested changing it. You can avoid re-exporting them by incrementing your prefix. So, 171183 would be the prefix used for all 2 digit decks you make, and 171184 for all 3 digit decks. That'll solve the conflict without needing to manually correct all of the previous files.
(Riiak, I'm not sure if you watch this thread, but if you do, do you know if an ID that long will cause problems?)
EDIT: Also, sorry I missed you on the chat. I was out of town for the day.