Thus, Java 1.6.0_29 is installed to your machine.
Is it a 64bit or a 32bit version?
I recommend to open a command prompt (cmd) and type the following command, to check it:
java -version
If you see something like that, it means your JRE is 64bit.
java version "1.6.0_23"
Java(TM) SE Runtime Environment (build 1.6.0_23-b05)
Java Hotspot (TM) 64-bit Server VM (build 19.0-b09, mixed mode)
Marvin Beans 64bit installer supports only 64bit java.
If your Java is not 64bit, please install a 64bit java version.
In the directory where you installed Marvin Beans package (C:\Program Files\ChemAxon\MarvinBeans is its default location), you will find an ".install4j" folder. In this folder, please check "inst_jre.cfg" file. Installer and uninstaller retrieve the location of java from this file.
This file should looks like this:
C:\Program Files\Java\jre6
If Java does not exist under the above location (that inst_jre.cfg refers), modify the file to point the real Java directory.
After that, uninstall should work.
If msketch.bat (C:\Program Files\ChemAxon\MarvinBeans\bin\msketch.bat) does not work, please check its config file.
The C:\Program Files\ChemAxon\MarvinBeans\bin\java.ini file is the config file for command line script that describes the location of java for them.
Java-Path=c:\program files\java\jre6\
It may refer to a non-existing Java path. In this case, fix the path. After that, msketch.bat should work.
Probably, the simplest way to fix this issue is the uninstallation of current Marvin Beans package and install it again.
At the new installation, installer check your system again and set references to your current Java in the config files of applications.