Steps to repro:

1. Download http://reports.qa.atl.jboss.com/binaries/RHDS/builds/nightly/3.0.1.GA/201005190307/installer/jbdevstudio-linux-gtk-3.0.1.v201005190307R-H69-GA.jar (or newer from http://reports.qa.atl.jboss.com/binaries/RHDS/builds/nightly/3.0.1.GA)
2. java -jar jbdevstudio-linux-gtk-3.0.1.v201005190307R-H69-GA.jar
3. when asked, enter a new folder for installation
4. see screenshot - installation proceeds into default folder, ~/jbdevstudio

Conversely:

1. Download http://reports.qa.atl.jboss.com/binaries/RHDS/builds/stable/3.0.0.GA/201003100055/installer/jbdevstudio-eap-linux-gtk-3.0.0.v201003100055R-H50-GA.jar (or equivalent from http://reports.qa.atl.jboss.com/binaries/RHDS/builds/stable/3.0.0.GA)
2. java -jar jbdevstudio-eap-linux-gtk-3.0.0.v201003100055R-H50-GA.jar
3. when asked, enter a new folder for installation
4. see screenshot - installation proceeds into custom folder