Execution plan issue requires reset on SQL Server 2005, how to determine cause?
Probably Parameter Sniffing. To troubleshoot this without running Profiler

1) Add a GUID into the text of the query as a comment. e.g.

/*ED7446E4-03B1-4279-AB43-6FFE800AD860*/


2) Wait for the problem to recur so that it runs slow from the application and fine from SSMS. 

3) Compare the query plans for the 2 different environments (retrievable from the below)

SELECT *
FROM   sys.dm_exec_cached_plans cp
       CROSS APPLY sys.dm_exec_sql_text(plan_handle) t
       CROSS APPLY sys.dm_exec_query_plan(plan_handle) qp
       CROSS APPLY sys.dm_exec_plan_attributes(plan_handle) AS epa
WHERE  t.text LIKE '%ED7446E4-03B1-4279-AB43-6FFE800AD860%'
       AND epa.attribute = 'set_options'