I know there are a lot of these topics around but none seem to help in my case, nor describe it exactly. The best similar one is aapt not found under the right path.
My problem is that I can be using Eclipse for a whole evening programming, compiling and using my device, and then suddenly I get "error executing aapt" for my current project and ofcourse R.java isn't (properly) generated anymore. I then restart Eclipse and everything goes away. I'm seeing this once a day on average however.
I've recently switched to amd64 and installed the latest Android-2.3 SDK and matching tools. I know that there is now a platform-tools folder that has an aapt version that should work SDK version independently. At first I had added this directory to my PATH, as instructed on the SDK website. I've also tried not adding it to my path and making a link platforms/android-9/tools so that every SDK version might use it's own old copy. Needless to say, platform-tools/aapt is there and has the right permissions, and I have been able to execute it on the command-line at any time.
When I do write a faulty xml file or sorts, and appropriately get an error, I see an extra line that says "aapt: /lib32/libz.so.1: no version information available". I'm running a recent Gentoo linux system. I have everything installed to support x86 on amd64, but have re-emerged emul-linux-x86-baselibs and zlib just to be sure. The problem persists. I do see some pages that spell horror over some zlib bugs, but I'm not sure if that's related. I realize I'm not on the reference Ubuntu platform, but surely the difference cannot be that great?
It might very well be a bug in aapt or the tools itself. Why would it suddenly stop working? I also experience that the ids in R.java were incorrect, name