"Generating dSYM file" takes ages in XCode 4.5
a dSYM file is used to resymbolicate your crash reports from users. Check out this Apple Tech Note, specifically the "Analyzing Crash Reports" section).
To speed things up, you could always turn off dSYM generation for your DEBUG builds and then turn it on for ADHOC and/or Store builds. Here is a related question that talks a bit about that.
dsymutil's run time is largely determined by the amount of debug information it needs to process to create the dSYM. Chances are you are using a different compiler in Xcode 3.2.6 vrs. Xcode 4.5, or the 4.5 compiler is emitting more/better debug information so the dsymutil time is longer.