Very hard to tell. If the checkboxes are native ones:
<input role="checkbox" name="myCheckbox">
And NVDA does not announce them then you have found a problem. Sometimes however the web developer has decided they don't like the styles provided by browsers for checkboxes, or they want some additional control in these cases you are likely to see something like:
<div role="checkbox" aria-checked="true" cclass="ckbx uncheck"></div>
Notice how this element has a role this is telling the screen reader hey you know that nondescriptive element div in this case treat it like a checkbox and then the aria-checked attribute in there lets the scree reader know if the checkbox is checked. However, Generally web developers use the "class" attribute to change appearance of elements, and if their Java script updates the class, but does not update the aria-checked you will get as you described, and there is nothing a screen reader can do about this since there are no standards on class and the picture that is changed when the class changes has no attributes and therefore no way to describe it.
Again, one can look at the attributes for this element in either the browsers developer tools, or using the NVDA F1 key sequence and looking at the last couple of lines shown. There should be an attributes line that lists the attributes the browser is providing to the screen reader like tag Name, role etc.

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