It is not clear from your description whether it is an Eclipse or Android SDK problem.
Try running aapt directly from the console (gives usage help) and check out the required libraries with ldd aapt. Ldd output looks something like following:
.../android-sdk-linux_x86/platform-tools$ ldd aapt
linux-gate.so.1 => (0xf7712000)
librt.so.1 => /lib32/librt.so.1 (0xf76b8000)
libpthread.so.0 => /lib32/libpthread.so.0 (0xf769e000)
libz.so.1 => /lib32/libz.so.1 (0xf7689000)
libstdc++.so.6 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/32/libstdc++.so.6 (0xf759a000)
libm.so.6 => /lib32/libm.so.6 (0xf7574000)
libgcc_s.so.1 => /lib32/libgcc_s.so.1 (0xf7559000)
libc.so.6 => /lib32/libc.so.6 (0xf73fd000)
/lib/ld-linux.so.2 (0xf76f6000)
Notice that although the system is 64-bit aapt links in 32-bit libraries. This is what the ia32-libs package is for. So if you find appt runs fine on the commandline it must be an Eclipse problem.
