The checkbox has to be connected to a field. It needs to have a value list item assigned. If you have that setup properly you can easily use a checkbox for finds.
How is your checkbox setup?
I completely understand your desire to be able to find ad hoc subsets of data. Long ago I decided that it was something my users did so often that I should just always provide a standard method of doing it, so now I build into every single table I create a field called "Tag", of type Number, with validity check set to insist that it have a value from the value list "One", which contains only the value "1". I format it as a checkbox (narrow enuf that the label "1" doesn't even show) and have 2 buttons that will (1) do a "Replace Field Contents" with "1"s on all the "Tag" boxes in the current found set and (2) find all the checked "Tag" boxes, with an option (if a modifier key is held down) to clear them all.
It sounds as if the situation you're facing is that you may have a mismatch between the field type and the value in your own equivalent of a "Tag" box. FileMaker will look for all Text fields that have something in them by using an "*" as the Find criterion, but it looks for all Number fields that have something in them with a different method, ">0".
What are the values you've assigned to your check boxes?