Yes, it can cause problems and/or performance issues. MyISAM in nearly all cases will fall short of InnoDB and only offers minor faster reading (select queries) and has full-text indexes (not an issue for MYSQL 5.6+). Any frequent inserting, updating, or deleting will cause significant slowdowns compared to InnoDB. The worst issue is MyISAM does full table-locking, but InnoDB only locks the row. There's many more reasons to use InnoDB over MyISAM (the table locking issue being the most serious problem; it can corrupt tables pretty easily if a query is interrupted). Joomla is InnoDB now and CBs engine will always follow Joomlas.
With that said I don't see how CB being InnoDB could cause your issue. I do not suggest changing the engine, but rather suggest the developer of your software fix their software. In short no one should be using MyISAM anymore with Joomla.
Kyle (Krileon)
Community Builder Team Member
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krileon
