We've seen this before and it seems to happen when something interferes with the communication between your computer and our server. I've seen it with all the computers behind the same external IP address as well as with individual computers. Is there some program (anti-virus or otherwise) monitoring your internet connections? If so you should whitelist PrimeGrid. As far as what you're calling "ghost units", they'll time out and be reassigned to someone else. They're not hurting anything here.

There don't appear to be any widespread problems with reaching our server. We have very little downtime since moving to RackSpace and all the downtime we do have is connected to keeping the server up-to-date (we can't run BOINC when we're updating MySQL, etc.). And some updates require reboots. Other than that I'm not aware of any problems.

Anything can cause this, including the widespread DDOS attack that has recently been causing widespread connectivity issues on a good chunk of the Internet. Unfortunately, although there's a "fix" for this, the cure is much worse than the disease.

If the server sends tasks to your computer but they don't get to your computer for any reason, the tasks will stay in limbo until they time out. There's nothing that can be done about this, sorry.
____________
My lucky number is 75898⁵²⁴²⁸⁸+1