Summary:

We got some support queries over the weekend from various customers who were upgrading their wordpress installs saying that they were having permissions issues.

Resolution:

I've been dealing with the installatron guys for the last 4 or so hours and we've tested and re-tested and ... so on. We've got the bug nailed down now and I've successfully upgraded from 2.0.5 on a customers blog to latest stable available without breaking permissions.

I've a feeling this also sorts another issue for the upgrade that looses files that were changed during an upgrade.