I'm using one of the nightly builds of Mozilla and it seems that the pipelining has been mostly fixed. There's still a problem with it sometimes having trouble if you stop a page in the middle of loading and then load another page - Mozilla still tries to reuse connections which have old requests queued up on them.
They've also fixed another annoying bug that would randomly cause some pages to load twice - it could be hard to notice, but on some pages you'd see two requests in Proxomitron's log window. It could cause double posts at some sites too.
As far as the persistence goes it works fine, but you may be having the local file problem described in the other posts. Disabling local persistence will avoid that, but using the filter should work better.
Funny that there's not much consistency in the symptoms people describe as causing this - for example, some were reporting turning off local persistence actually made the half-loads worse. Since many things - both Proxomitron related and not - can cause partial page loads, I suspect it may not all be the same issue.