I have no experience with teh 1dMkII but my experience with PCs/electronica in general would suggestt aht rather than just taking the batteries out and putting them back in, try the following:
Remove battery.
Remove lense [and put dust cap on for obivous reasons]
Remove button cell battery.
Remove CF card.
Hell, remove anythign you can 
Set on worktop, leave for half an hour while you ahve a cup of tea with biscuit of choice. Check over any accessories you ahve to see if any of the contacts are dirty or misaligned with the body/lense/battery etc. Watch you don't get crumbs in there now.
Go back, put button cell [preferably the new one] back in.
Put battery [hopefully fully charged, obviously] back in. But nowt else. no CF card, no lense, nowt.
Turn on. See what happens.
A lot of electronic equipment has capacitors to trickle feed to the main boards, and you do have to give them a few seconds [or more - I have seen my PCs BIOS settings stay teh same for up to a minute with teh battery out] to fully lose any settings that might be causing problems.
Hence even if you have changed batteries, for something like this, leave it off for a good while before reinserting, that guarentees that it will fully reset.
If that doesnt work, I'd suggest getting it sent back to vendor/warranty folks and getting it looked at professionally.
If it works, then try adding the CF card, then a lense without the CF card, then the lense AND CF card, etc to try to work out where it is falling over.
As I say thats more experience with complex electronics than with cameras per se, but cameras are complex electronics so the basic rules still apply overall. Remove ALL power sources, ALL accesories, leave for half an hour, and 'bare boot' the item with no accessories at all. then troubleshoot from thereon in.
HTH 
NB: You havent left the CF door slightly open have you...? Don't know if that affects the 1DMkII....it bloody well does on my 300D...