Premiere Pro CS6 extreme project bloating and Media Encoder

This is a bug that I noticed first in CS5 and it hasn't changed in CS 6.0.1. It's recently reared it's head again as an editor I'm working with has been playing with Media Encoder and recreated the problem at the expense of our current project file being usable.

Here's what's happening: We have a 20MB or so commercial project, no warp stabilizer, no frequent "save as" stuff going on. We've been exporting sequences by opening up Media Encoder and using the "add Premiere Pro Sequence" feature. Works great. The only drag is that it can take a while for the Dynamic Link to load the project so you can pick which sequences to encode.

The editor did some reading online and found you can click and drag sequences from Premiere into the Media Encoder. I warned him against this because I had tried it previously in CS5 and 5.5 and found that it would give you really slow project save times and auto save times, which seemed to stem from exponentially growing project file sizes.

In the hopes that the problem had been fixed, he went ahead and used the click-drag technique a couple times. Now we have a 3.71 GB project file that won't open and seemingly, so far, won't import into a new project.

This is catastrophically bad. We have clients coming in tomorrow, have a short turnaround, and can't open our project or import it into a new project.

Anyone have similar experiences? Any way to clean out the bloat from these projects?

In case this helps, here are my machine specs:

Mac Pro 2.66 GHz 12-core Mac Pro
16GB RAM
NVidia Quadro 4000
ATTO Fibrechannel
Blackmagic Design Decklink Extreme 2

Thanks in advance for any advice.

Best,
Jon

"If you can describe what it is, that's not it."