So I'm in a league where I have set my rotation to Starter 1 and then Starter 2a and Starter 2b.  Starter 1 will get the first start, followed by Starter 2a then Starter 1 again and then Starter 2b. 

Starter 2a started his game and I put Starter 1 on rest.  I was thinking that the logic would then have Starter 2b pitch the next game. My reasoning is that the SIm would want to chose Starter 1 next, but there is no Starter 1 and since Starter 2a just pitched a game the next pitcher in line to start would be Starter 2b.  Instead, however Starter 2a ended up getting the start again.  Is this a glich or am I missing the logic here?

It will probably end up screwing me out of a playoff spot seeing Starter 2a is tired from just pitching the day before. I reduced his pitch count and put Starter 1 in as a setup man, but who knows if that will work out. 

I suspect that when you put starter 1 on rest, you essentially 'reset' your rotation.  A "glitch" is in the eye of the beholder.  I would say it is at least a programming "miss".  It definitely violates the "principle of least astonishment".  

When you rested starter 1, sparky looked to the next available starter. If starter 2a had been below is auto rest number, Sparky would have bypassed him and gone on to 2b. Since he wasn't, Sparky started 2a.

You should have started with them set as starters #1, 2 and 3.............and then shifted to the 1, 2A/2B rotation when you were ready.

I'm curious what their fatigue settings were.....If he pitched 6 innings on opening day, the sim figured that he's on pace for over 900 innings, so he'd be very fatigued. In a setup like that you would be better off to use your AAA guys to start some of those games, give your regulars a chance to ease their way into the season. You can have them ready in relief, and with a high pull setting on the AAA guy you can keep him on a short leash if you like. Watch those pitch counts, especially early in the season....Why put him on rest in the first place? If he's below your fatigue setting then sparky won't use him anyway...

This was a theme league with no AAA.  Ed Walsh was my SP1, Bob Gibson was my SP2a and Maddux my SP2b.  What I should have done was switch Maddux to SP1 and Walsh to SP2b while Gibson was about to pitch his game. Instead I rested Walsh.  I wanted Maddux to be my next pitcher in line. Pfattkat, great advice. I could have changed Gibson's Autorest so he would not have started. With all of this said, I reduced Gibson's pitch count ot 70 and had Walsh availabe as a setup A and I ended up winning the game anyway. 

I set it up this way because I was experiencing some bullpen fatigue throughout the season--mainly because I started the season while I was on vacation and the 3-4 days I was gone royally screwed up my 'pen.  So I wanted Maddux and Gibson to be able to go deep into games and I figured Walsh could be my one starter who could handle pitching every other game and the bullpen would be used most when he pitched. It worked out pretty good.  My bullpen rebounded from the fatigue and since it had worked so well for my team, I simply kept the rotation in place.