I suggest using a separate field with one checkbox for each such value in your set of check boxes. Then they will export cleanly to Excel, the order clicked won't matter and if you group the fields together, they will still have the same "look and feel" of a single field with a group of check boxes.
You can use a bunch of replace field contents operations to do a "one time fix" to move the data from your existing check box field into the newly added separate fields.
In some cases, it even pays to go one step further and make your set of check boxes indivdiual records in a related table, but I don't see a reason for this in what little I can deduce in this post.
I did come up with a solution for this (sorry, again, a year later)...
One of the uses I had for translating one field's values into separate columns was to make a class roll.
I was able to keep all the class enrollments in one field.
Then, I had to create separate fields for EACH class and calculate their value as such:
If ( PatternCount (— 1Fall Classes; "FRI - Bal 3-6;") ≥ 1; "X" ; "" )
Then I made a layout that made a matrix of the enrolled students, those calculated fields above for each class, in each row.
It worked for me, and I think I might be able to adapt this to other uses for separating out a check box's contents.
However, this was very time-consuming to set-up. It was a huge help, though, once it was set-up.