Hi folks- have a look at this link for a free programme for testing whether you markers are good together (and whether they produce primer dimer and hairpins). Anyone embarking on multiplex or having problems currently should have a look at this. It is obvious that some markers just do not seem to work in multiplex and you may be able to screen these oligos/combinations out before you start (e.g. Carl Vangestel found that the program highlighted that the pigtail on one of his markers was the problem- by replacing it with non-pigtailed he managed to get it to work nicely). Alex Ball (+ others?) is using this so if you need a quick instruction ask him.
(AutoDimer: a screening tool for primer-dimer and hairpin structures. Biotechniques. 2004 Aug;37(2):226-31)