I have been using AE for many years now, largely for TV work, but recently I have been doing more feature work.
When starting a render, I have noticed the machine is quiet, chugging along, tearing through the render at a decent clip. Coming back an hour or so later, I can hear the machine's hard drive going nuts and the render speed significantly slower, with the "Estimated Remain" figure significantly higher than originally estimated. I've noticed this consistently regardless of whether the content being rendered is multi-layered comps with numerous various elements and effects, or if it is just reprocessing numbered DPX frames. I have also noticed this happens regardless of whether I am rendering to a Quicktime movie or numbered frames in DPX or TIFF format.
My machine is a MacPro, with 2 x 2.93GHz Quad-Core Intel Xeon, 8Tb internal HDD, 32Gb 1066 MHz DDR3 RAM, running OSX Lion 10.7.2, Adobe After Effects CS5 (10.0.2.4), which has memory set to multiple processor rendering.
I have juggled RAM allocations to other apps (even though the only other thing running is the OS - everything else is off), juggled the number of processors that AE is to use, and numerous other memory and cache settings, but consistently AE at some point into these renders decides using RAM isn't the thing to do any more and chooses instead to use the hard drives. I would have thought 32Gb of RAM would have been a good amount for AE, but I get the decided impression it has rarely employed it.
I read there's a default usage of 2Gb RAM, but this has been upped in AECS5.5 to 20Gb, so that may solve the problem, true, but until I can upgrade, I'm wondering if this problem might be something else.
Any experienced wisdom is welcome.
What memory and multiproccessing settings have you tried?
Look for Todd Kopriva's post on recommended settings and try them.
Have you run some sort of system monitoring software and watched how your system's usage is behaving during a render?
Here's a link to the FAQ entry that Szalam mentioned:
It sounds like you're swapping the contents of RAM to the disk. That is a performance killer. The FAQ entry has a link to a post by me about that. The gist is to leave plenty of RAM for the OS and other software.