I had the same issue for a different purpose. the WF in SPD see the boolean fields from a form or from library columns as YES, No only " even if the field contains TRUE, FALSE". It is smart enough to treat this conflict with form fields but it can't treat it for library columns and maybe there are other scenarios.
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What I did as the solution is to lets the boolean fields in a form or in the library to be number integer with values 0, 1. no one can argue about 0 or 1 values included SPD. [ you can let the number integer field to have min value to be 0 and max 1, this to guarantee that it will be only 0 or 1].
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this is a very powerful solution, as I think, especially when the boolean field used to determine loop condition or IF condition that includes many many actions inside.
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Please try it and let me know