I'm also having the problem with 1.3.9c...

It seems that all my customers who have brought this to my attention are using FF, and then when they switch to another browser, all is well.

My thought is that it could be stale cookies, but I'm not sure.

The few customers that have told me experienced this when using PayPal as their payment method. When PayPal returns them to my site, they get a Login Time Out error.