Since a couple of versions back the trunk version has a lot of problems with construction queues for trucks. Often (in the latest version, almost all of the time) the whole gui hangs when you shift-click to construct several buildings after the other. This has happened to me with any building, but you most often encounter it when you try to build several VTOL rearming pads (since that's when you use the function most, as you cant just hold and drag a field to build them on like you can do with walls, but have to place every pad by themselves). I think I started to get the problem in some trunk version released last week, and has happened in every version since.
The whole gui hangs, you can't click any buttons, issue any orders or anything, though you can still move the pointer around and you can see that the 3D world lives on, all units that already have orders are doing what they should.
The only way I've found to get out of the hanged gui is to repeatedly press the right mouse button and esc, after some time either the gui starts working again with the truck totally ignoring to build the structure you wanted it to make and instead move to the position you had the mouse pointer at when everything gets working or the menu background pops up (without any content, that is, no options to select, just the blue square) which you can escape out of and the game works again.
Desktop: AMD Athlon X3 440 3.0ghz, 4GB RAM, Radeon HD4200, Windows 7 Professional 64-bit
Laptop: AMD Athlon X2 QL-64 2.1Ghz, 3GB RAM, Radeon HD3200, Windows Vista Home Basic 32-bit & Ubuntu 9.04 64-bit