it can be it or other things you do w/ your acc as well
i mean how hard would it be for them to check the authorized apps within your acc if they want, manageflitter unfollows hundreds of people in a matter of seconds and as per twitter TOS aggressive follow churn is not allowed
but how about trying a few days w/o manageflitter to see if the locking is happening w/o it as well or not
i remember seeing others saying too that they get locked more frequently lately (not related to manageflitter), so maybe twitter just strictened their overall rules, they were well long enough one of the easiest platform in the hands of spammers