We have a related issue where it appears the preload routines get stuck in an endless loop. I can see the same sequence files continually popping up over and over and over again and what used to take no more than 5 minutes on 2010 we have let run for 30 minutes and canceled it with it still running. We definitely have some sequence files where A will call a subsequence in B and B will call a subsequence in A and I just wonder if the analyzer is somehow just looping over and over again when it does this.
This is new for 2012, we didn't have this type of issue with 2010 SP1.
Edit: Btw, clicking anywhere in the Sequence Editor while this is happening typically results in the application going unresponsive. Pulling up the Task Manager (WinXP) shows SequenceEditor is using a full core (50% CPU) of my dual core cpu.