mostly I am doing fine with the default 1000ms.
The problem can occur in bigger environments in combination with complex solutions i.e with multiple WSP files to be deployed.
On deployment SharePoint is distributing the WSPs to all servers in the farm and installing them. Normally the deployment MSBuild task checks all servers in the farm if the deployment has been completed successful. But after a certain timeout we made it to
continue anyways, so that the deployment script does not end up being stuck in an endless loop (important for automatic deployments ie. through TFS). In this case your described issue could occur.
Setting the timeout to more seconds might help you to resolve the issue but it is hard to say which delay is best in general.
So if you are experiencing these problems, you can just increase it step by step.
As you are probably not deploying that often to the production environment (at least not on a daily basis) you could also override the delay with a higher value i.e 10s only for the specific environment (similar to the samples in ParameterDefault.msbuild
for the SiteUrl).