I have found that most of my problems have cleared up by doing the following :-
1. Adding the following to /etc/initramfs-tools/modules :-
ohci_hcd ehci_hcd
2. Rebuilding the initramfs by running 'update-initramfs'
3. Reboot.
This (I believe) ensures the modules are loaded in the right order at boot.
I have found that most of my problems have cleared up by doing the following :-
1. Adding the following to /etc/initramfs- tools/modules :-
ohci_hcd
ehci_hcd
2. Rebuilding the initramfs by running 'update-initramfs'
3. Reboot.
This (I believe) ensures the modules are loaded in the right order at boot.