Have you checked wait stats?

I got into the habit of using the below query for initial investigation into performance related prolems:

This is from Paul Randals blog: http://www.sqlskills.com/blogs/paul/

WITH [Waits] AS

(SELECT

[wait_type],

[wait_time_ms] / 1000.0 AS [WaitS],

([wait_time_ms] - [signal_wait_time_ms]) / 1000.0 AS [ResourceS],

[signal_wait_time_ms] / 1000.0 AS [SignalS],

[waiting_tasks_count] AS [WaitCount],

100.0 * [wait_time_ms] / SUM ([wait_time_ms]) OVER() AS [Percentage],

ROW_NUMBER() OVER(ORDER BY [wait_time_ms] DESC) AS [RowNum]

FROM sys.dm_os_wait_stats

WHERE [wait_type] NOT IN (

N'CLR_SEMAPHORE', N'LAZYWRITER_SLEEP',

N'RESOURCE_QUEUE', N'SQLTRACE_BUFFER_FLUSH',

N'SLEEP_TASK', N'SLEEP_SYSTEMTASK',

N'WAITFOR', N'HADR_FILESTREAM_IOMGR_IOCOMPLETION',

N'CHECKPOINT_QUEUE', N'REQUEST_FOR_DEADLOCK_SEARCH',

N'XE_TIMER_EVENT', N'XE_DISPATCHER_JOIN',

N'LOGMGR_QUEUE', N'FT_IFTS_SCHEDULER_IDLE_WAIT',

N'BROKER_TASK_STOP', N'CLR_MANUAL_EVENT',

N'CLR_AUTO_EVENT', N'DISPATCHER_QUEUE_SEMAPHORE',

N'TRACEWRITE', N'XE_DISPATCHER_WAIT',

N'BROKER_TO_FLUSH', N'BROKER_EVENTHANDLER',

N'FT_IFTSHC_MUTEX', N'SQLTRACE_INCREMENTAL_FLUSH_SLEEP',

N'DIRTY_PAGE_POLL', N'SP_SERVER_DIAGNOSTICS_SLEEP')

)

SELECT

[W1].[wait_type] AS [WaitType],

CAST ([W1].[WaitS] AS DECIMAL(14, 2)) AS [Wait_S],

CAST ([W1].[ResourceS] AS DECIMAL(14, 2)) AS [Resource_S],

CAST ([W1].[SignalS] AS DECIMAL(14, 2)) AS [Signal_S],

[W1].[WaitCount] AS [WaitCount],

CAST ([W1].[Percentage] AS DECIMAL(4, 2)) AS [Percentage],

CAST (([W1].[WaitS] / [W1].[WaitCount]) AS DECIMAL (14, 4)) AS [AvgWait_S],

CAST (([W1].[ResourceS] / [W1].[WaitCount]) AS DECIMAL (14, 4)) AS [AvgRes_S],

CAST (([W1].[SignalS] / [W1].[WaitCount]) AS DECIMAL (14, 4)) AS [AvgSig_S]

FROM [Waits] AS [W1]

INNER JOIN [Waits] AS [W2]

ON [W2].[RowNum] <= [W1].[RowNum]

GROUP BY [W1].[RowNum], [W1].[wait_type], [W1].[WaitS],

[W1].[ResourceS], [W1].[SignalS], [W1].[WaitCount], [W1].[Percentage]

HAVING SUM ([W2].[Percentage]) - [W1].[Percentage] < 95; -- percentage threshold

GO