This one has been tough to figure out because the Thinkify connection/programming code has been touched for many years. However because of this latest clue about checking/unchecking the option to store reader info in the database it gave me a different angle to look at this.
Checking/Unchecking that option was probably just removing your Motorola (or other primary readers) from the list of readers - which left only the Thinkify reader as the Active reader to try and use. I just discovered that the software was essentially getting stuck trying to use the first active reader (even if it was not connected). Again, what's odd is that it doesn't appear that any of that code has changed either in many years.
I just fixed the issue, you can test it out with the new 1.6.4.2 beta version by
clicking here if you'd like. 1.6.4.2 is basically done, my twins will be using it for a XC race this afternoon and a road race this weekend. The only thing left I hope to add in is the ability to pull in Athletic.net CSV files and I'm waiting on them to finish testing the live results export to their website. So hopefully the official launch of it will be early next week. 1.6.4.2 has a lot of great improvements and it's the last update I hope to push out until things slow down after the Fall season.
If you'd prefer to stay on the version you're currently on, try simply marking your other readers as "inactive" in the Settings screen. If that doesn't do the trick, you can remove it, program your tags, and then re-add it (or check or uncheck the option to store reader info in the database). Just remember to add it back, enable it, or undo that option when you want to use your primary reader.
Sorry for any headaches this has caused, but thankful it will be fixed with the next update.