I'm working with sun java desktop ( ;-) ) and installed the latest J2EESDK as
root. When I start netbeans as a regular user and create an application server,
it's getting the scripts for pointbase wrong.

1) As you can see the *.sh are not executable. This if you want to connect to a
db instance from within netbeans, it don't work, because it cannot execute
startserver.sh. The scripts in
/opt/netbeans-4.1/SunAppServer8.1/pointbase/tools/serveroption/ are fine.

2) The pbenv.conf is wrong as it can be. Looks like a copy&paste from some
else's preferences.
* The AS_POINTBASE should point to /opt/netbeans-4.1/SunAppServer8.1/
* There is no user "ludo" on that machine!
* There is nor never has been a JDK 1.4.2_06 installed. (There's an
/opt/jdk1.5.0_04 and an /usr/java/jdk1.5.0_05)

more details:

andreas@linux:~/.netbeans/4.1/pointbase/tools/serveroption> ll
total 44
-rw-r--r-- 1 andreas users 194 2005-11-28 08:57 pbenv.bat
-rw-r--r-- 1 andreas users 148 2005-11-28 08:57 pbenv.conf
-rw-r--r-- 1 andreas users 457 2005-11-28 08:57 startcommander.bat
-rw-r--r-- 1 andreas users 374 2005-11-28 08:57 startcommander.sh
-rw-r--r-- 1 andreas users 453 2005-11-28 08:57 startconsole.bat
-rw-r--r-- 1 andreas users 374 2005-11-28 08:57 startconsole.sh
-rw-r--r-- 1 andreas users 538 2005-11-28 08:57 startserver.bat
-rw-r--r-- 1 andreas users 456 2005-11-28 08:57 startserver.sh
-rw-r--r-- 1 andreas users 478 2005-11-28 08:57 stopserver.bat
-rw-r--r-- 1 andreas users 403 2005-11-28 08:57 stopserver.sh
-rw-r--r-- 1 andreas users 15 2005-11-28 08:57 stopserver.sql
andreas@linux:~/.netbeans/4.1/pointbase/tools/serveroption> cat pbenv.conf
AS_POINTBASE=/opt/SUNWappserver/pointbase
AS_POINTBASE_SAMPLESDB=/home/ludo/.netbeans/dev/pointbase
PB_CONFIGURED_JAVA_HOME=/usr/java/j2sdk1.4.2_06
andreas@linux:~/.netbeans/4.1/pointbase/tools/serveroption> ls /usr/java/
j2re1.4.2_08 j2redefault jdk1.5.0_05
andreas@linux:~/.netbeans/4.1/pointbase/tools/serveroption> echo $JAVA_HOME
/usr/java/jdk1.5.0_05
andreas@linux:~/.netbeans/4.1/pointbase/tools/serveroption> cat
/opt/netbeans-4.1/SunAppServer8.1/pointbase/tools/serveroption/pbenv.conf
PB_JAVA=/opt/jdk1.5.0_04

if [ -d "$PB_JAVA" ] ; then
PB_CONFIGURED_JAVA_HOME=$PB_JAVA
elif [ -d "$JAVA_HOME" ] ; then
PB_CONFIGURED_JAVA_HOME=$JAVA_HOME
else
echo "JDK for Pointbase needs to be configured. Refer to
$AS_POINTBASE/tools/serveroption/pbenv.conf"
exit 1
fi

# To Configure JDK for Pointbase:
# Either modify this file with proper value of PB_JAVA or set JAVA_HOME to point
to JDK 1.4.2_x in the environment before running Pointbase. For detailed
information, consult documentation.