if you map 'Inventory' to "Mouse 3" (middle-click) and then open your inventory, middle-clicking will not close it (even though middle-clicking just worked to open your inventory).
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also on Ubuntu 13.04 amd64 in minecraft 1.6.2
java version "1.7.0_25"
OpenJDK Runtime Environment (IcedTea 2.3.10) (7u25-2.3.10-1ubuntu0.13.04.2)
OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode)
and the problem also applies to button 6 and 7 the side scrolling.

Is this still a concern in the latest Minecraft version 14w08a? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.

Still an issue in 08a and 1.7.5

Confirmed for 14w18b.

Confirmed for 14w25b.

Confirmed for 1.9-pre1
Confirmed.