How do you have this update page setup in regards to the update server behavior and the MRT server behavior that is applied to it? Please describe as best as you can what is currently going on with this page and how you have set it up. Please also post back with a copy of the page in question in a zip archive so that we can take a look at it.
Normally on these pages you would have a recordset that is used to set the value of the checkboxes to the id, then the checkboxes should be in a repeat selection area for MRT to make use of them.