If I've understood you, it really boils down to whether the interactive application you need to integrate has been developed according to an educational scoring standard such as SCORM, AICC, QTI etc. If so, it should be straightforward to import it directly into Chamilo (via the learning paths or the tests tool) and learners' results will be automatically integrated into Chamilo's Assessment/Gradebook facility. If not, there's no "point-n-click" way to integrate the scores generated into Chamilo (or any other LMS for that matter - that's the whole point of SCORM/AICC etc.)
You'll have to reconstruct the activity as a SCORM course, using an external SCORM compliant application, or within Chamilo.
It may be worth taking a look again at the "Tests " tool, particularly the questions options. It may be less limited than you think. Bear in mind that each question option (and it's a pretty comprehensive range) includes a pretty powerful rich content wysiwyg editor (with an html option) so that a "Test" can really be a scored interactive lesson.
If you're looking for more interactive-graphical input (e.g. drag and drop matching) Hot Potatoes is well worth a look. It's an open source option that offers a range of options, and will export exercises as a SCORM package. Chamilo allows for the option of uploading Hot Potatoes exercises in the Tests tool. There's plenty other tools (some quite pricy) for producing SCORM compliant content which you can import to Chamilo, including:
Accent, Accenture, ADLNet, Articulate, ATutor, Blackboard, Calfat, Captivate, Chamilo, Chamilo 2, Claroline, Commest, Coursebuilder, Docent, Dokeos, Dreamweaver, Easyquiz, e-doceo, ENI Editions, Explio, Flash, HTML, HotPotatoes, Hyperoffice, Ingenatic, Instruxion, iProgress, Lectora, Microsoft, Onlineformapro, Opikanoba, Plantyn, Saba, Skillsoft, Speechi, Thomson-NETg, U&I Learning, Udutu, WebCT
All this assumes you're just looking at automated scoring - if there's tutor input to the course then the options you need are all in the "Assessments" tool.
All the best,