Are you trying to select an item from a combo box on the website?
I had the exact same issue just now, and managed to get around it by replacing the Html modelled combo box element with an AA modelled one, using the ""window press keys"" action to send the required value to the combo box.
It seems the combo box was executing a javascript function called onchange=reloadapplet(this.value) which when invoked after using the Html action ""Select Item"", caused the Application modeller to ""loose"" its html capabilities.
Once I changed the navigate stage to utilize the AA element instead of Html, everything started working fine again.
No idea why yet... but it seems to me like it's some sort of bug in BP Application Modeller.
Hope this helps.
Andrzej Silarow