The writing of changed preferences only happens on normal quit of Cross. This has always been the case.
Crsahing during autoplay and analysis likely are related. I haven't seen anyone reporting this kind of issue with autoplay. I've run it for 100's of hours without issue.
There can be many causes for a track to have some kind of issue resulting in a corruption message. If you have crash files please provide to
support@mixvibes.com so the error code can be added to the exceptions. If possible also provide an associated track file so the issue can be duplicated.
With repeating corruption usually a similar source of the tracks is involved.
Your issue with the MCP is not clear if this is MIDI or sound related. If sound please use the ASIO4ALL driver and set this to use the MCP. By this you can use the 64bit version of Cross.
In this situation analyzing non-analyzed tracks before using autoplay is recommended as this would clearify what causes the crash.