No armor proficiency and no armor equipped giving Disadvantage

[Asmerion]

I verified that the FGU is applying Disadvantage to any ability check, saving throws and attacks that use Strength or Dexterity performed by characters who do not have armor proficiency, even when they do not have any armor equipped.

[Moon Wizard]

Assuming you are talking about 5E, the armor proficiency check box is purely to tell FG whether a PC is proficient in the armor they are currently "wearing".
If the PC is not wearing any armor, then they are technically proficient in the "armor" they're wearing (i.e. nothing), and you should leave the armor proficiency box checked.

Regards,
JPG