disk I/O error in SQLite
That sounds like a problem with the shared drive arrangement, rather then one specific to sqlite. It would be worth stating which virtualisation method you are using as people may know if there are common problems with it.

The slower run from a resourse within the VM may be due to I/O overhead from the virt method, or extra IO contention because the input data was on a different physical drive to the VM. It may also be that the guest OS is memory starved, which will increase IO contention for large inputs as they can't be held in cache as easily on the host with it's larger memory. Again more detail would be needed for a surer answer.

Of course both problems could imply an intermittent IO error, so check you OS logs and the drives' SMART readings.

(this is likely to get more traction on serverfault, as it is likely not database specific)