Scilab installed but application does not start
If you are right about it being OS compatibility then yes installing the latest version which works fine for me on Yosemite should work.

To answer your question about the upgrade: If I remember correctly scilab is a standard Mac install via a .dmg and drag the application to the Applications folder.

If this is the case then just download the latest .dmg from here - http://www.scilab.org/download/5.5.1 (make sure to download the one verified for 10.10), mount it and copy the application to the Applications folder overwriting the previous version. And now it should work. Let  me know if it doesn't.