This one's kind of a funny one.

qmake is built with qt. In most cases, it refers to $startdir/src/.../qmake, so it runs it fine. When it gets to the plugin directory, it tries to refer to qmake without the full path. Since I'm building on a machine without qt, this doesn't work.

Quick fix would be to set your PATH before hand to include the directory that qmake is built in $startdir/src/$pkgfqn/bin. Less hackish solution would be to figure out why qt was using the absolute path sometimes and not others.

After testing my fix I found the problem with the PKGBUILD. It seems that qmake wasn't found because the QTDIR variable that's set in the PKGBUILD is incorrect. It should be 'export QTDIR=$startdir/src/$pkgfqn'.