You've probably installed hsqldb version 1.8.x rather than 1.7.x on your server (see deployment instructions - section 1.6).
Since Tersus Studio comes with 1.7.x bundled, the database created by the embedded server for each project (which is the files in the project's 'database' folder) is in 1.7.x format (and incompatible with later versions).
To overcome this download 1.7.3 from the download link in the deployment instructions, replace the existing hsqldb.jar in your deployment with the one included in the archive you've downloaded, and restart tomcat.
Regarding your windows server 2003 question, I'm not sure I understand it. Deployment is along the same lines as the one you seem to be attempting right now.
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