I wouldn't be surprised if this was related to dynamic allocation on the VM. Essentially, it can inject a random very large I/O latency to any operation. It may also change the hardware model used by the VM.
I would recommend looking at InnoDB diagnostics, and possibly starting up w/ innodb_force_recovery=1 set in my.cnf. Run "check table" on each table (or at least the ones you've detected problems with) for closer analysis. --Joe
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