execution plan differences
blocking
check wait stats during execution
check file IO stalls during execution
sp_whoisactive (awesome freebie from Adam Machanic of SQLBlog fame) can really help you here
Or get a professional to remote into your system for about 10 minutes ... 😎
Best,
Kevin G. Boles
SQL Server Consultant
SQL MVP 2007-2012
TheSQLGuru on googles mail service