When creating a fixed size disk, VirtualBox will often lock up the entire system for several seconds. When this happens phpVirtualBox's watchdog thinks that an error has occurred and requests a page refresh. This results in an orphaned VM that doesn't show up in the web UI and must be manually removed. I can recreate this on CentOS 6 and Fedora 20 on different machines.
An option to increase the watchdog timer would be a simple fix. I manually increased the timer in eventlistener.js and the issue was resolved. I would be willing to submit a patch for a configuration option if you approve of this approach.