Sorry for replying late. No progress yet. :(

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Have you checked your Event Viewer for any warnings or errors arising from java or Unity?

I checked the event viewer for Windows Logs -> Application but did not find any Java or Unity specific logs. Are any other sections of Event Viewer which I should look into?

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And which version of Windows are you using?

Windows 7 x64
with,
Unity 3.3.0f4
Java 1.6 (x64 and x86) Update 26
JDK 1.6 (x64 and x86) Update 26
Device: Samsung Galaxy GT-I9000
Android: v2.2

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They also recommend deleting 3.X and ensuring that your phone is attached.

I have total four 2.X APIs and I my phone is always attached while building the application.

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Have you ever been able to build this project without killing java.exe in the process?

I have not been able to build any application without killing java.exe since the day I have installed Unity and Android pro. :|

Thanks,
Kranti

Have you checked your Event Viewer for any warnings or errors arising from java or Unity?

And which version of Windows are you using?

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Even deleting Android 1.X APIs as suggested in the following threads did not help:

They also recommend deleting 3.X and ensuring that your phone is attached. Along with this interesting piece of advice..

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Well, the latest beta seems to work properly with x64 Java and more than 6 Android APIs installed. But as a workaround, please try to keep less that 6 APIs in the sdk folder.

What you're describing implies that Unity actually has discovered the SDK resources, but is unable to load them following its subsequent call to java.exe. I think that Unity calls java.exe to build the app's Android layer and then performs a dex conversion on the resulting class files before packaging them. If you're able to complete the build by killing java.exe, it suggests that these resources are being built but not released by the java process - or Unity may simply be loading earlier builds from the file system. Have you ever been able to build this project without killing java.exe in the process?

http://forum.unity3d.com/threads/89269-Unity-freezes-when-Try-to-locate-Android-SDK
http://forum.unity3d.com/threads/71150-Unity-freezes-while-building-APK

Thanks,
Kranti

I've never run into this, but is the java.exe process running continuously - i.e. is it active before and after the call from Unity? Because it sounds as though it may not be releasing the SDK resource, which is preventing access by subsequent calls. What happens if you kill java.exe prior to attempting the build?