I have a hitter on my bench who's got 95 speed and 88 baserunning.  He's had great SB numbers the last few seasons, so I signed him for a bench/PR role this season.  My PR setting is at 3 and he's had two attempts through 4/5 of the season.  My basestealing setting is at 2, but smart speedsters (and he certainly qualifies) are not supposed to be affected by that.

Am I missing something?

Well, the base stealing setting does impact everyone, even the "smart speedsters" - it is not designed to kill their SB attempts entirely, but it does reduce them.

What is your pinch running setting? Do you have the individual settings set to allow only certain players to be pinch run for?

How many times has he come in as a pinch-runner in clear SB situations and not run?

I have my PR setting at 3.  I have three hitters set to "don't PR for".  Which means five hitters and a pitcher are eligible to be pulled.  This guy has 2 SB attempts in like 120 games.  I have to believe I've had more PR scenarios than that.  He's only appeared in 22 games...and he's started a couple of those.  It doesn't add up, to me.