I'm working with Analysis Office and have the above mentioned issue.
When I add a crosstab and reformat it, eg. remove a measure from the crosstab, press the "Prompt' button, give a variable value, then the removed measured goes back into the crosstab automatically.
In the components menu, the "set back on opening the workbook" is not ticked.
I encounter this issue in version 2.3 SP1 and SP2 as well.
Do you have any idea, why this happens?