Huh~ Very strange...
Unfortunately I can't test your exact scenario (no Captivate 6/HTML5), but when I tested it in 5.5 with a text entry box and an alert that calls the associated variable, it updates according to what I typed into the box. I didn't have to change any other settings or mess with On Focus Lost.
Have you tried a new project to just test that one aspect? What I did was insert a text box, associate a variable (testVariable) with it, and then on exit for that slide execute this code:
var objCP = document.Captivate;
alert(objCP.cpEIGetValue('testVariable'));
(Obviously you'd need to use the approriate syntax for HTLM5 in your case.)
You could also insert a text caption with the Captivate variable and set it to show all slides of your project. That way you can make sure it's being populated when you type into the text box, and that the Captivate variable isn't getting overwritten at some point further in the project.
Sorry I don't have any concrete suggestions, but that might help narrow it down even further.