There are ways to use a portal to display a scrolling list of check box values. It takes a bit of programming to implement, but sounds like the best option here. Comment had a very nice demo file for this. If you search the forum for "Scrolling Checkbox" you might be able to find a thread where he posted a link to this file.
One caution on your current design: If you remove a value from your table that serves as the source of values for your checkboxes, that value remains in your checkbox fields, but the format will hide the fact that this value is still in the field unless you examine an unformatted field for the value. This hiddent value can affect which records are found when you perform finds as filemaker may "find" the hidden text, but the checkbox formatting hides the text from view.
Thanks for your reply, I decided to re-plan my method as I could see a few issues with this method. I have now got it working well using a portal with Get related records (Mr Vodka pointed me in the right direction), it took me a while to figure it out and I nearly threw my pc in the bin a few times, but it was worth the effort as I learnt so much!