With such a jump in product versions it would be difficult to narrow down a specific change that has caused the differences that you are seeing.

I'm not sure why checksums would have changed - it is the CRC32 of the file so should be consistent between runs and across machines. Likewise, I'm unsure why on one machine the dev folder wasn't being picked up despite being specified

It does sound like an annoying issue has been resolved though, in that the location was configured but not honored as well as the checksums being different.

I think that, if you are sure the migrations haven't changed then you should run repair to get the new checksums into the Schema History Table.

You can also set locations for a specific environment using environment overrides: https://documentation.red-gate.com/fd/environment-flyway-namespace-277578926.html

For disclosure, I'm a developer working for Redgate on Flyway