Why query plan is different
This is the same type of behavior described in Erland Sommarskog's Slow in the Application, Fast in SSMS article, as well as my post, Multiple Plans for an "Identical" Query. The reason is that, even though the query text may be identical, SQL Server must generate independent plans due to the differences in set options. Sometimes this just leads to wasted space in the plan cache, but other times it can lead to completely different plans due to changes that have happened to the data in the meantime (especially if a long time has passed since the first plan was generated).
You can work around this by adding this to Plan Explorer's command text prior to the query text:
SET ARITHABORT ON; GO
Or by doing the opposite in SSMS (change ON to OFF).