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ACT 2013 - DB Maintenance caused SQL Query to become very slow??

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ACT 2013 - DB Maintenance caused SQL Query to become very slow??

I'm running the latest version of Sage Act! 2013 for Windows, I had a fairly complex SQL Query (Query with multiple sub-queries) I was running from MSSMS as ACTREADER user.  The query was taking about 10 seconds to complete before DB Maintenance.

I hadn't ran the DB Maintenance (Repair and Re-index) in quite some time so I decided to run that last night and it completed fine.
But now today when I run my SQL query and it's been running for over 14 minutes and has not completed execution or returned any data yet.

Is there an indexing issue or something here that might cause this?    I had read somewhere that reindexing and then updating table statistics (like act db does) can sometimes cause this type of issue.

Any one have any thoughts or experience with this type of issue?

Any help would be appreciated.
Thanks!