You can select which baseline to calculate Variance from in File > Options, Advanced - Earned Value Options (Project 2010) or Tools > Options, Calculation, Earned Value button (2007 or 2003).

You may also calculate Variance manually in spare Duration field. Use the formula:

ProjDateDiff([Baseline1 Finish],[Finish])

to calculate the finish variance using Baseline1 Finish.

I hope this helps.
Julie