Goodman Games

The physical armor check penalty reads "The physical check penalty applies to checks to climb, jump, balance, swim, move silently, and other such physical activities." Except half of those apply to skill rolls (d20+mod, DC's 5/10/15/20), while the other half, namely climb and move silently (which doesn't exist, but there is "Sneak silently" which sounds redundant) use d%. Does that mean thief skills are affected less by armor check penalties than other skills?

I would like to throw my hat in with the recommendation to standardize the thief skills with the standard skills.

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.

The notion that Thieves get the d% roll AND a regular Skill check is definitely something that needs to be highlighted in the rules. Also I think this d% roll just shouldn't be available if the Thief is wearing any armor besides Padded, Hide(?) or Leather. Thieves just shouldn't be allowed to make that extra roll.

Otherwise, I'd be concerned the conversion of standard bonus/penalty to a d% bonus/penalty would reach 4e levels of "wait, I'm +5%. No, wait, +10%. Now minus 15% for my armor..."

I think it's just easier to say that a Thief in plate mail just doesn't get to do that stuff.