Huh... what do you know, your suggestion to wait until after starting a new game and getting into the game itself actually worked. I usually DO activate the trainer at the menu screen since most games map a function to the F1 key and I'm too lazy to remap. It usually works; I've never experienced that before, not with prior versions of the Civ 5 trainer or with any of the several dozen other CH trainers I've used.
I guess that's why you're the expert! Thanks, Cal!
EDIT: Maybe a little blurb about this could be added into the official troubleshooting guide? Maybe under the "Have you tried running the trainer different ways?" section? I did try the suggestion to open the trainer after the game (which, of course, was a spectacular failure; couldn't even get it to hook), but never thought to try waiting until the game starts as opposed to activation on the menu screen.
instant research gives you tons of research points... you use them up as you queue the next research item.. the LAST trainer people complained they had to push the button over and over to make research complete... now i get people telling me that they don't like it the opposite way..
While it would be nice to have an option to reset research to 0, the entire idea behind that option is to get you the tech you want. If you don't want fast research, don't press it. Not trying to offend or insult, but frankly from what I've seen, the best games tend to be where you start from scratch against a lot of civs and you get the tech slowly through the marathon option (gives you a chance to work with what you got and learn the intricacies of the units). As pwiz and cal have stated numerous times for almost all trainers; use the options when you need to. If you don't need or want that huge boost, don't use it. Just my two cents.