I have my pitchers set on autorest at 95%, but it appears this feature is applied immediately after the previous game is played, not before they take the mound. 

To explain.  SP#4 already has the ball and is pitching the day before an off-day.  As such, I want to skip SP #5's turn in the rotation, so I flip the spot names of SP#4 and SP#5.  SP#1 is setting at 57(78), so i assume, after the off day he will be at an acceptable 78(99).  To me, this means SP#1 should have the ball after the off-day, but instead, it floats past SP#1, SP#2 and SP#3 (all at below 95%) and is handed to the pitcher I was trying to avoid - so I have four fully rested pitchers and some lame-*** throwing.

Would hope this could be fixed, but if not, I encourage anyone in  a similar situatio to do a work around by taking off the auto-rest feature if the ball is going to be handed off on an off-day.

It's not a bug.  It's been like that forever.  I questioned it before.    The ball is handed to the next pitcher BEFORE injury or fatigue recoveries.  That is how they programmed it. 

I run my staffs at 95-98% during the season but change them to 70-80% in the playoffs because of it.  I've had guys get skipped on off days because he hadn't recovered enough before the off day but would have been 100% by game time.

That is the response I received from customer service.  They can say its not a bug, but the logic is not logical.

It's logical in the sense that we can't name a starter right up until game time, like in MLB.  The next game's starter is determined immediately after the previous game ends, just as you said.  Otherwise people would be able to completely shuffle their rotation on the off day. 

I'm not saying I'd have a problem with that, but that's not the way HBD is designed.  They don't want unfair, last minute SP changes, so the guy is locked in as soon as the previous game finishes.

PS: You should see that situation coming in advance.  If your desired starter as at 78(99) with an off day coming up, then drop his autorest setting to 75 until he's made his start, then bump it back up.

I agree, the work around is fairly easy -- not tedious.  I, however, don't think it would be a problem to wait to name the next starter until the off-day cycle runs.   the way ti stands now, is your starter is in place for two HBD games if you have an off day, while your opponent is only locked in to one.  To me it would be an easy fix that still would not allow you to change at the last minute.  The real probelm with this happens in the playoffs (as noted by The Mike)