I doubt this'll be hardware related, I've seen interfaces get "stuck" quite often. First off I would seriously consider upgrading to 6.1(4) at least, 6.1(1) is not a good code to run, lots of issues with it. You cna also try a "failover reset" command to see if that'll bring the interfaces up into the proper mode.
In short, stop replacing hardware, I doubt that's the problem.