If my board filter uses the syntax "project in (PRJ1, PRJ2)", the board is listed in the JIRA 6.4 sidebar under the "Boards in this project" drop-down list.

If my filter instead uses the syntax "category = Myprojects", the boards are not visible.
If I use a sub-filter "project in (PRJ1, PRJ2)" and reference it using "filter = 12345 and..." it doesn't show up in the list either.

I don't see any good workaround, because when you have dozens of filters all based on the same "project group", having to manually change them one by one to modify the project list is just not usable.