Any eventhandlers firing when you check them? Perhaps you need to enable some of the additional event recording options. Check out the page source and see how things are defined. It should look something like:
I have seen this a lot in the code I am testing with.
Do the Checkboxes both have the same name in the Source Code? If so, what eTester is PROBABLY doing is checking the first box and then the check action for the second box is actually UNchecking the first box because the name is the same.
If this is the case then you will either need to base events on index, or use VBA code to find some other way to uniquely identify the checkboxes.