Render time Issues with 5.0 project in CC 12.1

This is actually a copy of a post I had in a different discussion entitled "render time" but this now
I did some extensive testing to try and see why my render times in CC were so much slower that 5.5 and I found some very interesting results.
The original project was created in 5.0 and opened in 5.5 and rendered, it contained video footage and graphics. When it was render in 5.5 it rendered in 4:27. When I opened it in 12.1 and rendered it was 18:00. I then started turning off layers and my render times shot up. basically layer 12 had two animated masks on colored solid. With this off it took 8:30
I then imported the project into 12.1 and saved it, reopened it and with layer 12 off it took 5:11. So importing and saving the project made a difference. Now I recreated layer 12 in 12.1 from scratch and turned it on and my rendered time was 6:50.
So there is something going on with projects being converted from earlier versions - Now to really test this theory I would need to recreate the project from scratch and compare to the 5.5 times.
To further test this we did the same sort of testing with a different comp and found similar results - the render times were different if it was imported vs. just opened. But the big thing we found with this comp was a layer where we were moving large stills with some z space. It looks like the 3d from 5.0 was causing a major slow down in CC on layers that has AE 3d applied.
I think the major take away is if your comp was created in 5.0 and you need to modify it, then make changes in 5.5 or 5.0 or be prepared to recreate any layers with more than simple key frames.
Just to also answer some other questions - in rendering to prores vs. animation or dvcprohd the times were almost the same. The animation was slightly longer but that makes sense cause the file was much bigger.
I also found that with 32 gigs of ram my magic number was 11 reserved for other apps ...
Hope someone can jump in and add some light to this
This was all done on a 2010 mac pro 2.66 w 12 cores 36 megs ram running 10.8.4 - I have 5.5 and CC and the 12. 1 updates are installed and the video card is an NVidia 575. Mulit threading was on and in 5.5 - 9 Megs is reserved and in 12.1 - 10 is reserved

I've experienced similar problem with Java Web Start twice.
Also using JRE version 1.5.0_06 Java HotSpot(TM) Client VM and Browser Internet Explorer 6.0.2800.1106 on Windows XP (Problem was the same with Java 1.4.2)
My application was signed and launched via JNLP. The security warning popup was shown in the windows taskbar, but it was hidden. Using maximize in the taskmanager, I was able to see the dialog but it was blank. The problem was persistent, although I did not try as many times as 20-30 :-)
On both occations the problem occured on multi (3) screen systems, which I suspected to be the problem (Java has historically had some issues regarding multi screen systems), but now I'm not so sure.
Did you find a solution / cause?

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