If the adaptive junk mail detection feature is off, the "When I manually mark messages as Junk" section of the Junk mail controls is disabled. It should enabled. See also related bug 299826.

Duplicate of bug 230110 -> Suite bug 217528 / bug 233281?

Uh, no. It's not the same as those bugs. This is a bug about options being grayed out when the adaptive junk mail detection is disabled from the Adaptive Filter tab of the junk mail controls. Hence its different from bug 230110 and bug 233281. As for bug 217528, that's a Application Suite bug and has nothing at all do to with Thunderbird.

With the new division of junk controls (coming in TB 2.0 -- see bug 257990) the problem as described no longer occurs: the "When I manually mark..." controls, now found under Tools | Options | Privacy | Junk, is always enabled regardless of whether junk detection is enabled for any or all accounts. The issue described at bug 217528 still exist (in both TB and the suite), and is probably of interest to people following this bug.