I'm running Mint 14 amd64 with the Cinnamon desktop (currently at v1.6.7). One of the apps I use a fair bit is Frescobaldi, which is an editor for the Lilypond music engraving program. After installing Frescobaldi, I created a desktop icon by right-clicking on the Frescobaldi icon in the Cinnamon menu and selecting 'Copy to desktop'.
If I start Frescobaldi from the desktop icon, then right-click on a lilypond file in the file manager and select Open With / Frescobaldi, then the file opens in the already running instance, which is what should happen according to the way I have preferences configured in Frescobaldi. However, if I start Frescobaldi from the Cinnamon menu, and then open a lilypond file from the file manager, it starts a second instance and opens the file in that. This difference in behaviour between starting from the menu or desktop is completely reproducible with any lilypond file. I checked the properties of the two icons, and they execute exactly the same command: 'frescobaldi %F'
I also tested with starting Frescobaldi from an icon added to the Cinnamon panel, and it behaves the same way as starting from the menu - a second instance is started.
It seems to me that the problem must be in Cinnamon rather than in Frescobaldi if starting it from the two locations with exactly the same command results in the behaviour being different.