I am using a VPS, and was thinking up upgrading from Apache 2.2.25 to Apache 2.4.6
Are you saying I should not do this?
No, I don't think he meant that. He just expected those timestamp related errors for this use-case, because...
The plugin won't work well in a multi server environment as it writes files to the filesystem. That's why each server has a different timestamp as the files are stored on each.
I wouldn't recommend WPSC on a load balancing environment, either.