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Issue with query against large dataset in Spring '13

I have a managed package that has been running successfully referencing a business object that in some cases has over 2 million rows.  Prior to Spring'13 there was no issue.  With Spring'13 the query consistently fails with an error saying that the 100000 row limit has been exceeded.  Has anyone else seen this?  Have you found a solution?


 I opened a case a couple of days ago but other than pass it from one rep to another around the globe, there has been nothing done on this.