Thanks for the follow-up, Gregr. I was curious to hear what you found. Are there any visibly identifiable differences in the electronics of a Thomas that does work vs. one that does not? The older RF-style Thomas engines should all use the same communication channel and communication syntax. It may be frequency drift in a given engine (works with the original remote, but too-far off for the Universal Remote), or as you suggest, there might be some version difference between production runs, although I am not aware of any.
We'd certainly appreciate any further info you could provide.
Thanks,