If it is any consolation, I have the same problem. Extract by Attribute worked fine in ArcMap 10.0 but no longer works under 10.1 when comparing other than the first two fields in an input attribute table in your sql expression.
Other new V 10.1 problems I've found:
It the output from GetCount is Zero, the result often cannot be assessed because statistics are no-longer calculated for an empty output dataset.
If the output of Calculate Value is Zero, it cannot be assessed because V10.1 MB now confuses a valid output value of Zero to be the same as FALSE. If you want to iterate based on more than one value, you will be stopped from entering Calculate Value to evaluate your expression if one of the values you wish to evaluate has gone to Zero and you have set this value as a precondition for Calculate Value.
Version 10.0 used to avoid this by creating (what I call) an implied dependency if your Calculate Value expression included an in-line substitution (%Variable%), but this has gone away in 10.1. Now, if any of your in-line substitutions go to Zero and your expression is dependent on that value via precondition, you can't evaluate it because the precondtion goes to False. You often can't remove the precondition, however, because it is your only means of controling the logical flow of the model.
This has left me stranded for the time being in converting my 10.0 model to 10.1.
