SQL 2005, After relocated DB, App performance drops dramatically!!

This is the story, We have just relocated DB to a brand new SAN, but one application drops performance / take twice as much time to run reports!!

In the previous environment where DB stored on the old SAN, everything was okay, but because of the growing rate of the DB, our workplace bought a brand new SAN / fiber channel Harddrives + super IO controllers, faster spin Harddrives, more space capacity and such.

There are 2 apps (both apps exist on same servers). connect to SQL 2005 DB, (same DB) once we relocated the DB to a new SAN, App1 performs 5 times faster, but App2 runs very slow, it takes twice as much time than it normally would to complete generating reports (we run this app everynight). We haven't changed anything to the app servers (in term of hardware or OS) or app coding, the only change we made was REINDEX the DB, Could this be a problem?

Where should we start looking for the cause of the problem?
Appreciate your comment/suggestion, Thank you..