Hello,
this might be a reson, although I am not quite sure why it should have so in some cases.
On this site - artio.net, we also use "main" language and AFAIK the checkout process works fine.
Anyway, in JoomSEF 3.6.2, there also have been added additional checks the improve behaviour and solves some redirect problems when there is a main language configured. Also, it should now work even when JfRouter is left Active, but still the recommended setting is to turn it inactive.
Sp maybe you could try upgrading to the latest JoomSEF (if you have not done so yet) and report whether you still need to have the main lanaguage set to none or not.