The synch procedure can be tricky, especially with 2 keys, but sounds like you might have battery/circuit board issues with the remotes as well.
Are you SURE BOTH keys were working perfectly before?

If I remember correctly the second key gets synched right after the first without doing the ignition cycle again.

__________________
1988 325is (purchased new) sold
2004 X5 3.0 2005 X3 2.5
2008 X5 3.0 (new to me)