Yesterday I created a deployment job, for our system tester, that deployed from one box to another within our domain. Everything worked fine but overnight it decided that our farm administrator account was not an administrator!
After rebooting the boxes it accepted the account but would not deploy, throwing the usual 'helpful' error messages into the log files and event logs. As it was the development environment I tore down the site on the WFE and recreated the job and ran it - guess what no luck. It seemed that my 'error' was to recreate the WFE site on the same port number, by changing this the deployment worked. This doesn't fill me with confidence for when we move to our staging environment and ultimately production.
I'm guessing that with the issues with workflow and deployment have cost the project over 15 days to date. So I would suggest that in your project plan to add some extra days for these kind of gotchas.
So I'll end this post with a 'thank you' to the developers of the deployment and workflow process for all the helpful error messages that must be getting thrown but never caught!