Good catch! The thief skills used to be d20 based, but I switched them around a couple months ago to the % system. The player reaction is usually a love it / hate it thing. Something I should have clarified in the rules is that thieves get their % check in addition to
the D20 check for a skill. For example, if a wall requires a DC 15 Climb check, the thief can attempt their %, then, if that fails, take the normal d20 check. But to get back to your original question, please multiple the "-1" or "-2" armor penalties by 5% to get the appropriate thief penalty. Hope that helps.
Thieves never wear armor, though -- at least never in my games -- so it probably won't come up in your games.