I went through a similar thing when Caresuper merged with Spirit super last year. A month or so with the account locked.
It didn't cause me any grief, but surely they could speed up these processes.
Caresuper has currently locked its Direct Investment option for about a month while it changes its provider for this service. It was well flagged, but is still too long and this time its coincided with a period of high volatility in the markets.
I suspect it isn't just an IT matter. A full audit, including one involving processes, is probably required and may involve outside bodies such as APRA. It would not surprise me when these situations occur, external audits are necessary.