So the problem is basically when I get to encoding my five or more sequences (each of the sequence has a dinamically linked AE composition within), AME CS5.5 usually gets stuck in the process (after successfully encoding the first sequence). It does not respond to any command and no, there are no programs running in the background. I tend to close PPRO when I start encoding my projects. The usual formats I use are SD AVI (PAL) with "match sequence settings" enabled, and H264 MP4 (also SD-PAL).
How can I fix this?
i7-2600 3.40 Ghz
Quadro 2000D (GPU acceleration is enabled in PPRO CS5.5)
Windows 7 Home Premium SP1
Try either disabling GPU acceleration in PPRO before exporting to AME or queuing up only one job at a time.
There's a lengthy thread here on the forums about similar issues with AME CS5.5. One big thing to keep in mind is that the hang on AME's side is just a symptom--a result of a problem upstream--and there have been a number of different issues that all resulted in AME hanging while encoding. We fixed several of these issues in CS6, but at least a few known cases remain. So it's worth downloading the trial version of PPRO CS6 to see if your case is fixed.
Also, there are subtle differences in the particulars of the hang, such as whether it hangs in about the same spot with a given sequence--if so, then there's probably something about assets or effects/transitions at that point that is triggering the issue. If AME hangs at different points in a given encode, then it might be a resource issue on your system, such as RAM getting maxed out.