You need Java 7 (because Java 6 will not work). OpenJDK should be OK. Java errors are dumped to server-error.txt.

Something is very wrong

Check if the singlepage-mode parameter is set up correctly in the headers, as explained here.

Formulas are mixed up

Do you have to singlepage scribble files in the same directory? See Avoiding Conflicts

Execution of the command “scribble ...” freezes

If your talk has many formulas, and this is the first time you are executing the scribble command, you may need to wait 1 min or so... But sometimes it, really, freezes. This may happen on slow machines. Do the following:
1. Stop scribble (just Ctrl-C)
3. rm formulas.sqlite
4. rm formulas/*
6. Start your scribble command again