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Well, having an external drive partitioned into three drives is always going to slow things down... and FAT32 is not even close to the best file system format for video footage... is your other media (XDCAM, AVCHD) also on this drive? Or is it elsewhere? My bet would be that you've got a drive problem...
Also, I'm assuming that you've properly copied over the full file structure of the P2, and not just grapped the clips out of it?
Most of the media I use is copied to the data partition on an internal drive.
There is no issue with speed as I tested copying a file over to the drives in question and hit roughly 70mbps without an issue - so this should rule out drive speed being the significant factor.
However I've tested the drive(s) on another workstation with the same software configuration and lo and behold the P2 files come across as they should do.
Probably something to do with my hardward configuration on the machine in question, not sure if it would be the mobo or processor...hoping very much that there's another workaround! On the underperforming machine (let's call that machine1) I have a quad core intel Q9550, 16gb of RAM and an nVidia GEforce GTX 470. 1 internal hard drive with 2 partitions; OS and data.
The machine that runs perfectly (machine2) has a QuadroFX1800, Xeon X3450 and 8GB of RAM. 2 internal hard drives - OS (128gb SSD), and data.
Looking at the problem it seems to me that it's either the older processor or the OS drive which is causing the problem. Oh, and to answer your question, there's no issue with the structure of the media, that's all been retained.
I would say absoultely your issue lies with your hard drive configuration. Having two drives is a minimum requirement for PrPro to run effectively, and that means two actually physically separate drives, not one drive with multiple partitions. In fact, my understanding is that one drive with multiple partitions will operate even more slowly than one drive just by itself with no partitions.
Invest in a new drive for that system (or if you can't add an internal one, get an external eSATA for your data and projects) and you should see a huge difference in performance.
When I import P2 files located on my Maxx Digital 8TB raid with Areca Controller into Premiere Pro 5.5 it is instantaneous. But when I copy from the P2 cards to that raid the process does take a while. One process is actually copying all the data while the other is just setting up pointers to the file on my raid array.